From 4d95e4403f5cb73a87d212b8ebc1e991f8301ae2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 10:19:18 +0100 Subject: [PATCH 001/431] adding easyconfigs: MitoZ-2.3-foss-2018b-Python-3.6.6.eb, ETE-3.1.1-foss-2018b-Python-3.6.6.eb, tbl2asn-20190117-linux64.eb --- .../ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb | 32 ++++++++++++++ .../MitoZ-2.3-foss-2018b-Python-3.6.6.eb | 43 +++++++++++++++++++ .../t/tbl2asn/tbl2asn-20190117-linux64.eb | 35 +++++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8d2e3a53a51 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['870a3d4b496a36fbda4b13c7c6b9dfa7638384539ae93551ec7acb377fb9c385'] + +dependencies = [ + ('Python', '3.6.6'), + ('lxml', '4.2.5', versionsuffix), + ('PyQt5', '5.11.3', versionsuffix), +] + +download_dep_fail = True +#use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1c4cf8f66a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,43 @@ +easyblock = 'Tarball' + +name = 'MitoZ' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/linzhi2013/MitoZ' +description = """MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), + assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome + (genbank file as result), and mitogenome visualization.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/linzhi2013/MitoZ/raw/master/version_%(version)s/'] +sources = ['release_MitoZ_v%(version)s.tar.bz2'] +checksums = ['13fc5d3c6f41a6eb17498dfb1e69735a2b3f4e62ac7393d3ed71ea9502038841'] + +dependencies = [ + ('Python', '3.6.6'), + ('Perl', '5.28.0'), + ('Java', '1.8', '', True), + ('libgd', '2.2.5'), + ('Biopython', '1.72', versionsuffix), + ('BioPerl', '1.7.2', '-Perl-%(perlver)s'), + ('BLAST+', '2.7.1'), + ('HMMER', '3.2.1'), + ('BWA', '0.7.17'), + ('SAMtools', '1.9'), + ('Infernal', '1.1.2'), + ('ETE', '3.1.1', versionsuffix), + ('tbl2asn', '20190117', '-linux64', True), +] + +sanity_check_paths = { + 'files': ['MitoZ.py'], + 'dirs': [], +} + +sanity_check_commands = ["MitoZ.py --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb new file mode 100644 index 00000000000..461aa3042e9 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'tbl2asn' +version = '20190117' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/'] +sources = [{'download_filename': 'linux64.tbl2asn.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] +checksums = ['1f41acb9eacd6e0fa78657b17727b8f94d97490617563686d28b3f6c24d39117'] + +cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] + +files_to_copy = [ + (['tbl2asn'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn'], + 'dirs': [], +} + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +moduleclass = 'bio' From f39c3dc573b0f4328b96588323925d46497a04a7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Sep 2019 12:45:39 +0200 Subject: [PATCH 002/431] Amber: Fix incorrect checksum for Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch --- .../Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- .../Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- .../Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb | 4 ++-- .../Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb index 3e74a41ecc8..170c43234bd 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb @@ -66,7 +66,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb index 73b794ca79d..40a87660e18 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb index 190a8891827..be9476e4ce4 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb @@ -45,7 +45,7 @@ checksums = [ '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch - '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch @@ -64,7 +64,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch ] diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb index 4b6e40474b0..a193ea831d3 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb @@ -65,7 +65,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch From f2e6ab94716f64069e49b11d102225d6c604e2ae Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Sep 2019 13:09:51 +0200 Subject: [PATCH 003/431] Amber: Add missing builddep on flex --- .../Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb | 4 ++++ .../Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb | 4 ++++ .../Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb | 4 ++++ .../Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb | 4 ++++ 4 files changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb index 170c43234bd..a981a6dbf9e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb @@ -75,6 +75,10 @@ checksums = [ '129752ba327559951d79abc3d7d15fe919897b063edcd29f79112861bdd8d9ec', ] +builddependencies = [ + ('flex', '2.6.4'), +] + dependencies = [ ('netCDF', '4.6.1'), ('netCDF-Fortran', '4.4.4'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb index 40a87660e18..acfe7e1e18e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb @@ -79,6 +79,10 @@ checksums = [ 'b870417a0aad5b220dca9f590ec5cf857e06f44b7ee43165c4ace9901ae9a0f7', # Amber-16_test_cuda.patch ] +builddependencies = [ + ('flex', '2.6.4'), +] + dependencies = [ ('netCDF', '4.6.1'), ('netCDF-Fortran', '4.4.4'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb index be9476e4ce4..966df592edb 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb @@ -69,6 +69,10 @@ checksums = [ 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch ] +builddependencies = [ + ('flex', '2.6.4'), +] + dependencies = [ ('netCDF', '4.4.1.1'), ('netCDF-Fortran', '4.4.4'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb index a193ea831d3..50efe1d1cc6 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb @@ -72,6 +72,10 @@ checksums = [ 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch ] +builddependencies = [ + ('flex', '2.6.4'), +] + dependencies = [ ('netCDF', '4.6.1'), ('netCDF-Fortran', '4.4.4'), From e0b1b96515dae8005304230c82039e56426bffec Mon Sep 17 00:00:00 2001 From: crubb Date: Thu, 9 Jan 2020 13:48:16 +0000 Subject: [PATCH 004/431] {bio}[foss/2019a] FIX 1.068 w/ MCR 2017b and FSL 6.0.2 --- .../easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb | 35 +++++++++ .../FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb | 77 +++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2017b.eb | 23 ++++++ 3 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2017b.eb diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb new file mode 100644 index 00000000000..a0f6e68f5a9 --- /dev/null +++ b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'FIX' +version = '1.068' + +homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' +description = """FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad +components can be removed from the 4D FMRI data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['http://www.fmrib.ox.ac.uk/~steve/ftp/'] +sources = ['fix.tar.gz'] +checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] + +dependencies = [ + ('FSL', '6.0.2', '-Python-3.7.2'), + ('MCR', 'R2017b', '', True), + ('R', '3.6.0'), + ('ConnectomeWorkbench', '1.3.2') +] + +# add the installation dir to PATH +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['fix'], + 'dirs': [''], +} + +# setup FSL_FIX_MCRROOT to point to the install directory of MATLAB's Compiler Runtime (MCR) +modtclfooter = "setenv FSL_FIX_MCRROOT $::env(EBROOTMCR)" +modluafooter = 'setenv("FSL_FIX_MCRROOT", os.getenv("EBROOTMCR"))' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..221a6263126 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,77 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.2' +versionsuffix = '-Python-3.7.2' + +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-%(version)s_Makefile_fixes.patch', + 'FSL-%(version)s_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz + '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +builddependencies = [ + ('Boost', '1.70.0'), +] + +dependencies = [ + ('libgd', '2.2.5'), + ('libxml2', '2.9.8'), + ('libxml++', '2.40.1'), + ('SQLite', '3.27.2'), + ('libpng', '1.6.36'), + ('Tk', '8.6.9'), + ('NLopt', '2.6.1'), + ('freeglut', '3.0.0'), + ('expat', '2.2.6'), + ('zlib', '1.2.11'), + ('VTK', '8.2.0', versionsuffix), + ('GSL', '2.5'), + ('Qwt', '6.1.4'), +] + +# FSLDIR needs to be defined when running postinstall to get the correct shebang +# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 +postinstallcmds = [( + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH ' + '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' +)] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +# Adding the bin from the virtualenv was the only way to get things working... +modextrapaths = { + 'PATH': 'fsl/fslpython/bin', + 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb new file mode 100644 index 00000000000..a0f9d1fb9af --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb @@ -0,0 +1,23 @@ +name = 'MCR' +version = 'R2017b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] +checksums = ['a01619b30f8cfd34a9a9cefe8323a2ada22a65722fc13b823dae36086ddd259f'] + +# disable MCR's stock libstdc++.so.6 +# https://www.mathworks.com/matlabcentral/answers/329796-issue-with-libstdc-so-6 +postinstallcmds = [ + 'mv "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6" "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6-backup"' +] + +moduleclass = 'math' From b0b638e07dd8f323a0a7cb286d3fe4ec2771fa8b Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 10 Jan 2020 00:23:01 +0000 Subject: [PATCH 005/431] http -> https --- easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb | 2 +- easybuild/easyconfigs/m/MCR/MCR-R2017b.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb index a0f6e68f5a9..bab6f9e6480 100644 --- a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb +++ b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb @@ -9,7 +9,7 @@ components can be removed from the 4D FMRI data.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = ['http://www.fmrib.ox.ac.uk/~steve/ftp/'] +source_urls = ['https://www.fmrib.ox.ac.uk/~steve/ftp/'] sources = ['fix.tar.gz'] checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb index a0f9d1fb9af..9e7e4577386 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb @@ -1,7 +1,7 @@ name = 'MCR' version = 'R2017b' -homepage = 'http://www.mathworks.com/products/compiler/mcr/' +homepage = 'https://www.mathworks.com/products/compiler/mcr/' description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" @@ -9,7 +9,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries toolchain = SYSTEM source_urls = [ - 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', + 'https://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', ] sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] checksums = ['a01619b30f8cfd34a9a9cefe8323a2ada22a65722fc13b823dae36086ddd259f'] From 3bb294955f7978e28f6eb1ec5d315a8d4a56316f Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 10 Jan 2020 19:00:27 +0000 Subject: [PATCH 006/431] Fix Python deps --- ....068-foss-2019a.eb => FIX-1.068-foss-2019a-Python-3.7.2.eb} | 3 ++- .../easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/FIX/{FIX-1.068-foss-2019a.eb => FIX-1.068-foss-2019a-Python-3.7.2.eb} (92%) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb similarity index 92% rename from easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb rename to easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb index bab6f9e6480..64c65e7125d 100644 --- a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb +++ b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'FIX' version = '1.068' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' description = """FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad @@ -14,7 +15,7 @@ sources = ['fix.tar.gz'] checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] dependencies = [ - ('FSL', '6.0.2', '-Python-3.7.2'), + ('FSL', '6.0.2', versionsuffix), ('MCR', 'R2017b', '', True), ('R', '3.6.0'), ('ConnectomeWorkbench', '1.3.2') diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb index 221a6263126..252fc0eecf6 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,7 @@ name = 'FSL' version = '6.0.2' -versionsuffix = '-Python-3.7.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" From 094251e8a87ac04e84cc9ee5212b51a18148453e Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 10 Jan 2020 19:28:16 +0000 Subject: [PATCH 007/431] Revert "Fix Python deps" This reverts commit 3bb294955f7978e28f6eb1ec5d315a8d4a56316f. --- ....068-foss-2019a-Python-3.7.2.eb => FIX-1.068-foss-2019a.eb} | 3 +-- .../easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/f/FIX/{FIX-1.068-foss-2019a-Python-3.7.2.eb => FIX-1.068-foss-2019a.eb} (92%) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb similarity index 92% rename from easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb index 64c65e7125d..bab6f9e6480 100644 --- a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb @@ -2,7 +2,6 @@ easyblock = 'Tarball' name = 'FIX' version = '1.068' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' description = """FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad @@ -15,7 +14,7 @@ sources = ['fix.tar.gz'] checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] dependencies = [ - ('FSL', '6.0.2', versionsuffix), + ('FSL', '6.0.2', '-Python-3.7.2'), ('MCR', 'R2017b', '', True), ('R', '3.6.0'), ('ConnectomeWorkbench', '1.3.2') diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb index 252fc0eecf6..221a6263126 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,7 @@ name = 'FSL' version = '6.0.2' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-3.7.2' homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" From f151fe3d482d3e467d0c468c36ae0fa0d3cbd191 Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 10 Jan 2020 19:28:53 +0000 Subject: [PATCH 008/431] Rename to FIX-1.068-foss-2019a-Python-3.7.2.eb --- ...X-1.068-foss-2019a.eb => FIX-1.068-foss-2019a-Python-3.7.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/f/FIX/{FIX-1.068-foss-2019a.eb => FIX-1.068-foss-2019a-Python-3.7.2.eb} (100%) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb similarity index 100% rename from easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a.eb rename to easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb From 645999ca1f6be72f224d4db502bfb82305f90d27 Mon Sep 17 00:00:00 2001 From: crubb Date: Fri, 10 Jan 2020 19:56:27 +0000 Subject: [PATCH 009/431] Revert the reversion of 094251e --- .../easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb | 4 +++- .../easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb | 3 ++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb index bab6f9e6480..900230af10b 100644 --- a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'FIX' version = '1.068' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' description = """FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad @@ -14,7 +15,8 @@ sources = ['fix.tar.gz'] checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] dependencies = [ - ('FSL', '6.0.2', '-Python-3.7.2'), + ('Python', '3.7.2'), + ('FSL', '6.0.2', versionsuffix), ('MCR', 'R2017b', '', True), ('R', '3.6.0'), ('ConnectomeWorkbench', '1.3.2') diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb index 221a6263126..9727e4613b4 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,7 @@ name = 'FSL' version = '6.0.2' -versionsuffix = '-Python-3.7.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" @@ -49,6 +49,7 @@ dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.2.6'), ('zlib', '1.2.11'), + ('Python', '3.7.2'), ('VTK', '8.2.0', versionsuffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), From 00ef557f2c20d41107fa3bbcdff40776c6596c36 Mon Sep 17 00:00:00 2001 From: crubb Date: Sat, 11 Jan 2020 12:07:42 +0000 Subject: [PATCH 010/431] Fix MCR-R2017b to work with ConnectomeWorkbench; Fix FIX version --- ...thon-3.7.2.eb => FIX-1.06.12-foss-2019a-Python-3.7.2.eb} | 2 +- easybuild/easyconfigs/m/MCR/MCR-R2017b.eb | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/FIX/{FIX-1.068-foss-2019a-Python-3.7.2.eb => FIX-1.06.12-foss-2019a-Python-3.7.2.eb} (96%) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb similarity index 96% rename from easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb index 900230af10b..b9881ded055 100644 --- a/easybuild/easyconfigs/f/FIX/FIX-1.068-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb @@ -11,7 +11,7 @@ components can be removed from the 4D FMRI data.""" toolchain = {'name': 'foss', 'version': '2019a'} source_urls = ['https://www.fmrib.ox.ac.uk/~steve/ftp/'] -sources = ['fix.tar.gz'] +sources = ['fix-%(version)s.tar.gz'] checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] dependencies = [ diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb index 9e7e4577386..3760b551395 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb @@ -17,7 +17,11 @@ checksums = ['a01619b30f8cfd34a9a9cefe8323a2ada22a65722fc13b823dae36086ddd259f'] # disable MCR's stock libstdc++.so.6 # https://www.mathworks.com/matlabcentral/answers/329796-issue-with-libstdc-so-6 postinstallcmds = [ - 'mv "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6" "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6-backup"' + 'mv "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6" "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6-backup"', + 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Core.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Core.so.5-backup"', + 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Network.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Network.so.5-backup"', + 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Xml.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Xml.so.5-backup"', + 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Gui.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Gui.so.5-backup"', ] moduleclass = 'math' From 4dcc664c6564a12132c1f01220a8ae3e1b898bdc Mon Sep 17 00:00:00 2001 From: crubb Date: Sat, 11 Jan 2020 12:22:49 +0000 Subject: [PATCH 011/431] Fix FIX version --- .../easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb index b9881ded055..d59ed4fb8b7 100644 --- a/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb @@ -1,7 +1,7 @@ easyblock = 'Tarball' name = 'FIX' -version = '1.068' +version = '1.06.12' versionsuffix = '-Python-%(pyver)s' homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' From 1592b025934205475900cad593367502d4361720 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 14 Jan 2020 12:03:57 +0000 Subject: [PATCH 012/431] Revert Python dependencies; add Boost dependency; remove modextrapaths (#9654) --- .../FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb | 25 ++++++++++--------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb index 9727e4613b4..66056cb0ee2 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb @@ -10,7 +10,7 @@ name = 'FSL' version = '6.0.2' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-3.7.2' homepage = 'https://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" @@ -21,8 +21,8 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] sources = ['%(namelower)s-%(version)s-sources.tar.gz'] patches = [ - 'FSL-%(version)s_Makefile_fixes.patch', - 'FSL-%(version)s_Build_extras.patch', + 'FSL-6.0.2_Makefile_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', 'FSL-6.0.1_Melodic-use-ifstream-good.patch', 'FSL-6.0.1_Fix_fsl_exec_script.patch', ] @@ -34,11 +34,8 @@ checksums = [ 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch ] -builddependencies = [ - ('Boost', '1.70.0'), -] - dependencies = [ + ('Boost', '1.70.0'), ('libgd', '2.2.5'), ('libxml2', '2.9.8'), ('libxml++', '2.40.1'), @@ -49,7 +46,6 @@ dependencies = [ ('freeglut', '3.0.0'), ('expat', '2.2.6'), ('zlib', '1.2.11'), - ('Python', '3.7.2'), ('VTK', '8.2.0', versionsuffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), @@ -69,10 +65,15 @@ modextravars = { 'FSLWISH': 'wish8.6' } +# # Adding the bin from the virtualenv was the only way to get things working... -modextrapaths = { - 'PATH': 'fsl/fslpython/bin', - 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', -} +# +# NOTE: This did after extensiv tests not apply to the 2019a toolchain, please see +# https://github.com/easybuilders/easybuild-easyconfigs/issues/9654 +# +#modextrapaths = { +# 'PATH': 'fsl/fslpython/bin', +# 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +#} moduleclass = 'bio' From 366c86e106488b118d5aa41f35d0834999732d91 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 15 Jan 2020 12:16:46 +0000 Subject: [PATCH 013/431] FIX: Switched from MCR to Octave (depends on #9680); Added specific R modules (party, coin); hard-code Python dep again; FSL: Add Boost as dependency; Remove modextrapaths (with warning, #9654); hard-code Python dep again --- ...-1.06.12-foss-2019a-Octave-Python-3.7.2.eb | 62 +++++++++++++++ .../FIX-1.06.12-foss-2019a-Python-3.7.2.eb | 37 --------- .../FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb | 78 +++++++++++++++++++ easybuild/easyconfigs/m/MCR/MCR-R2017b.eb | 27 ------- 4 files changed, 140 insertions(+), 64 deletions(-) create mode 100644 easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Octave-Python-3.7.2.eb delete mode 100644 easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb delete mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2017b.eb diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Octave-Python-3.7.2.eb b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Octave-Python-3.7.2.eb new file mode 100644 index 00000000000..6070d970996 --- /dev/null +++ b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Octave-Python-3.7.2.eb @@ -0,0 +1,62 @@ +easyblock = 'Tarball' + +name = 'FIX' +version = '1.06.12' +local_interpreter = 'Octave' +local_python_ver = '-Python-3.7.2' +versionsuffix = '-%s%s' % (local_interpreter, local_python_ver) + +homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' +description = """FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad +components can be removed from the 4D FMRI data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://www.fmrib.ox.ac.uk/~steve/ftp/'] +sources = ['fix-%(version)s.tar.gz'] +checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] + +dependencies = [ + ('FSL', '6.0.2', local_python_ver), + ('Octave', '5.1.0'), + ('R', '3.6.0'), + ('ConnectomeWorkbench', '1.3.2') +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# FIX depends on a specific, older version of the party package +exts_list = [ + ('coin', '1.2-2', { + 'checksums': ['d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb'], + }), + ('party', '1.0-25', { + 'checksums': ['d4206f594c6fca0ab6e2fae1649333083e7938d5ca995a038cc730b80edc5921'], + }), +] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', + 'R_LIBS': '', +} + +sanity_check_paths = { + 'files': ['fix'], + 'dirs': [''], +} + +# Set FSL_FIX_MATLAB_MODE here, since modextrapaths does not accept integers. +modtclfooter = "setenv FSL_FIX_MATLAB_MODE 2" +modluafooter = 'setenv("FSL_FIX_MATLAB_MODE", 2)' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb deleted file mode 100644 index d59ed4fb8b7..00000000000 --- a/easybuild/easyconfigs/f/FIX/FIX-1.06.12-foss-2019a-Python-3.7.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'Tarball' - -name = 'FIX' -version = '1.06.12' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX' -description = """FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad -components can be removed from the 4D FMRI data.""" - -toolchain = {'name': 'foss', 'version': '2019a'} - -source_urls = ['https://www.fmrib.ox.ac.uk/~steve/ftp/'] -sources = ['fix-%(version)s.tar.gz'] -checksums = ['bb10a24f28b3c26a382744faa127c1c7bf3167dc7a4f06da1aab89b58b74ac72'] - -dependencies = [ - ('Python', '3.7.2'), - ('FSL', '6.0.2', versionsuffix), - ('MCR', 'R2017b', '', True), - ('R', '3.6.0'), - ('ConnectomeWorkbench', '1.3.2') -] - -# add the installation dir to PATH -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['fix'], - 'dirs': [''], -} - -# setup FSL_FIX_MCRROOT to point to the install directory of MATLAB's Compiler Runtime (MCR) -modtclfooter = "setenv FSL_FIX_MCRROOT $::env(EBROOTMCR)" -modluafooter = 'setenv("FSL_FIX_MCRROOT", os.getenv("EBROOTMCR"))' - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..ef41e53b1a4 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,78 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-%(version)s_Makefile_fixes.patch', + 'FSL-%(version)s_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz + '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +builddependencies = [ + ('Boost', '1.70.0'), +] + +dependencies = [ + ('libgd', '2.2.5'), + ('libxml2', '2.9.8'), + ('libxml++', '2.40.1'), + ('SQLite', '3.27.2'), + ('libpng', '1.6.36'), + ('Tk', '8.6.9'), + ('NLopt', '2.6.1'), + ('freeglut', '3.0.0'), + ('expat', '2.2.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.15'), + ('VTK', '8.2.0', versionsuffix), + ('GSL', '2.5'), + ('Qwt', '6.1.4'), +] + +# FSLDIR needs to be defined when running postinstall to get the correct shebang +# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 +postinstallcmds = [( + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH ' + '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' +)] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +# Adding the bin from the virtualenv was the only way to get things working... +modextrapaths = { + 'PATH': 'fsl/fslpython/bin', + 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb deleted file mode 100644 index 3760b551395..00000000000 --- a/easybuild/easyconfigs/m/MCR/MCR-R2017b.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'MCR' -version = 'R2017b' - -homepage = 'https://www.mathworks.com/products/compiler/mcr/' -description = """The MATLAB Runtime is a standalone set of shared libraries - that enables the execution of compiled MATLAB applications - or components on computers that do not have MATLAB installed.""" - -toolchain = SYSTEM - -source_urls = [ - 'https://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', -] -sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] -checksums = ['a01619b30f8cfd34a9a9cefe8323a2ada22a65722fc13b823dae36086ddd259f'] - -# disable MCR's stock libstdc++.so.6 -# https://www.mathworks.com/matlabcentral/answers/329796-issue-with-libstdc-so-6 -postinstallcmds = [ - 'mv "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6" "%(installdir)s/v93/sys/os/glnxa64/libstdc++.so.6-backup"', - 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Core.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Core.so.5-backup"', - 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Network.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Network.so.5-backup"', - 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Xml.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Xml.so.5-backup"', - 'mv "%(installdir)s/v93/bin/glnxa64/libQt5Gui.so.5" "%(installdir)s/v93/bin/glnxa64/libQt5Gui.so.5-backup"', -] - -moduleclass = 'math' From 2c8d7ac6c7a66f7f256343af1ac1322bd62673b7 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 15 Jan 2020 12:27:34 +0000 Subject: [PATCH 014/431] Style cleanup (space after #) --- .../f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb index 66056cb0ee2..18e9016a156 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-3.7.2.eb @@ -71,9 +71,9 @@ modextravars = { # NOTE: This did after extensiv tests not apply to the 2019a toolchain, please see # https://github.com/easybuilders/easybuild-easyconfigs/issues/9654 # -#modextrapaths = { -# 'PATH': 'fsl/fslpython/bin', -# 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', -#} +# modextrapaths = { +# 'PATH': 'fsl/fslpython/bin', +# 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +# } moduleclass = 'bio' From c20b4c67556cedf120a437d97497cf869093b323 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 17 Jan 2020 12:07:35 +0000 Subject: [PATCH 015/431] Remove Python 2.7.15 eb --- .../FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb | 78 ------------------- 1 file changed, 78 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb deleted file mode 100644 index ef41e53b1a4..00000000000 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,78 +0,0 @@ -# This build still relies on the following libraries (or part of them) shipped with FSL: -# GDCHART, libprob, libcprob, cprob, newran, newmat -# Attempts to use externally built libraries failed. Worth trying again in the future... -# -# Some tools like icmp are missing since they are built with the fslpython_install.sh script -# which locally installs Miniconda and creates a virtual environment. This is too messy and -# an alternative solution is necessary to install them. -# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 -# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation - -name = 'FSL' -version = '6.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.fmrib.ox.ac.uk/fsl/' -description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" - -toolchain = {'name': 'foss', 'version': '2019a'} -toolchainopts = {'cstd': 'c++11'} - -source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] -sources = ['%(namelower)s-%(version)s-sources.tar.gz'] -patches = [ - 'FSL-%(version)s_Makefile_fixes.patch', - 'FSL-%(version)s_Build_extras.patch', - 'FSL-6.0.1_Melodic-use-ifstream-good.patch', - 'FSL-6.0.1_Fix_fsl_exec_script.patch', -] -checksums = [ - 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz - '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch - '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch - 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch - 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch -] - -builddependencies = [ - ('Boost', '1.70.0'), -] - -dependencies = [ - ('libgd', '2.2.5'), - ('libxml2', '2.9.8'), - ('libxml++', '2.40.1'), - ('SQLite', '3.27.2'), - ('libpng', '1.6.36'), - ('Tk', '8.6.9'), - ('NLopt', '2.6.1'), - ('freeglut', '3.0.0'), - ('expat', '2.2.6'), - ('zlib', '1.2.11'), - ('Python', '2.7.15'), - ('VTK', '8.2.0', versionsuffix), - ('GSL', '2.5'), - ('Qwt', '6.1.4'), -] - -# FSLDIR needs to be defined when running postinstall to get the correct shebang -# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 -postinstallcmds = [( - 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH ' - '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' -)] - -modextravars = { - 'FSLOUTPUTTYPE': 'NIFTI_GZ', - 'FSLMULTIFILEQUIT': 'TRUE', - 'FSLTCLSH': 'tclsh', - 'FSLWISH': 'wish8.6' -} - -# Adding the bin from the virtualenv was the only way to get things working... -modextrapaths = { - 'PATH': 'fsl/fslpython/bin', - 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', -} - -moduleclass = 'bio' From b737c6ed65d84c7956e8184a62328baf9811089e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Jan 2020 16:43:35 +0200 Subject: [PATCH 016/431] adding easyconfigs: netMHCIIpan-3.2-GCCcore-8.2.0.eb --- .../netMHCIIpan-3.2-GCCcore-8.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..91e7d3a93f0 --- /dev/null +++ b/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-8.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'Tarball' + +name = 'netMHCIIpan' +version = '3.2' + +homepage = 'https://www.cbs.dtu.dk/services/NetMHCIIpan/' +description = """NetMHCIIpan 3.2 server predicts binding of peptides to MHC + class II molecules. The predictions are available for the three human MHC + class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2).""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +# netMHCIIpan is proprietary software, but free for academcs +# It can be requested at https://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan +sources = [ + { + 'filename': '%(name)s-%(version)s.Linux.tar.gz', + 'extract_cmd': 'tar --strip-components=1 -xzf %s', + }, + { + 'download_filename': 'data.Linux.tar.gz', + 'filename': '%(name)s-%(version)s-data.Linux.tar.gz', + }, +] +checksums = [ + 'd03df3463d38dc8b22bd57ebf0eb2d9ed31b47eb88ca507735988dffcc8ec036', # netMHCIIpan-3.2.Linux.tar.gz + '35bc1ece91ca328a013bc7a419f83c7e9e5c943e279126835c9dfbf63186bddc', # netMHCIIpan-3.2-data.Linux.tar.gz +] + +dependencies = [('Perl', '5.28.1')] + +keepsymlinks = True + +postinstallcmds = [ + "sed -i -e 's|setenv[[:space:]]*NMHOME.*|setenv NMHOME $EBROOTNETMHCIIPAN|' %(installdir)s/netMHCIIpan", + "sed -i -e 's|setenv[[:space:]]*TMPDIR.*|setenv TMPDIR $TMPDIR|' %(installdir)s/netMHCIIpan", + "sed -i -e '1i #!/usr/bin/env perl' %(installdir)s/NetMHCIIpan-%(version)s.pl", + "mkdir -p %(installdir)s/man/man1 && mv %(installdir)s/netMHCIIpan.1 %(installdir)s/man/man1/", + "chmod -R +rX %(installdir)s", +] + +sanity_check_paths = { + 'files': ['netMHCIIpan'], + 'dirs': ['data'], +} + +sanity_check_commands = ['netMHCIIpan -h'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 2cc7a3d60929b7430e9e3bbc92d21da57f7aedf5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Mar 2020 00:49:53 +0200 Subject: [PATCH 017/431] adding easyconfigs: Alpha-20190607-foss-2019b-Python-2.7.16.eb --- ...Alpha-20190607-foss-2019b-Python-2.7.16.eb | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..a4bf824daae --- /dev/null +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,82 @@ +easyblock = 'Bundle' + +name = 'Alpha' +local_commit = 'e027eb0fea1e' +version = '20190607' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.lirmm.fr/~swenson/alpha/alpha.htm' +description = "Alpha is a tool designed for detailed comparative study of bacteriophage genomes." + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('BLAST+', '2.9.0'), + ('Clustal-Omega', '1.2.4'), + ('GenomeTools', '1.6.1'), + ('GTK+', '3.24.13'), + ('matplotlib', '2.2.5', versionsuffix), + ('networkx', '2.2', versionsuffix), + ('pydot', '1.4.1'), + ('PyGObject', '3.34.0', versionsuffix), + ('pygraphviz', '1.5'), + ('python-igraph', '0.8.0'), +] + +components = [ + ('pyinclude', '0f8a00b8c10c', { + 'easyblock': 'Tarball', + 'source_urls': ['https://bitbucket.org/thekswenson/%(name)s/get/'], + 'sources': [{ + 'download_filename': '%(version)s.zip', + 'filename': '%(name)s-%(version)s.zip', + 'extract_cmd': "unzip %s && mv thekswenson-%(name)s-%(version)s %(name)s" + }], + 'checksums': ['9dc9b2bafbfe7a694ff4025164dc6e356989ee89b914691457fb0a474fe66c9e'], + }), + (name, local_commit, { + 'easyblock': 'Tarball', + 'source_urls': ['https://bitbucket.org/thekswenson/%(namelower)s/get/'], + 'sources': [{ + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s-%(version)s.zip', + 'extract_cmd': "unzip %s && mv thekswenson-%(namelower)s-%(version)s %(namelower)s" + }], + 'patches': ['%s-%s_fix-email.patch' % (name, version)], + 'checksums': [ + 'a9a0857ee080864c0d187f1f537aebdb3a61e58dd555b97dffbf2c2d73465f2a', # alpha-e027eb0fea1e.zip + '342d5d37bcfc19a2487c3b08860adc4246736919948b1968f899b0c595d7125d', # Alpha-20190607_fix-email.patch + ], + }), + # PythonPackage is last to not have its source copied by Tarball blocks + ('progressbar', '2.5', { + 'easyblock': 'PythonPackage', + 'source_urls': [PYPI_SOURCE], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['5d81cb529da2e223b53962afd6c8ca0f05c6670e40309a7219eacc36af9b6c63'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +postinstallcmds = [ + 'ln -s ${EBROOTGENOMETOOLS} %(installdir)s/%(namelower)s/lib/gtdir', + 'cd %(installdir)s/%(namelower)s/lib/ccode && ln -s bin_x86_64/eqclasses.so eqclasses.so', +] + +sanity_check_paths = { + 'files': ['alpha/%s' % x for x in ['alpha', 'analyzeblocks', 'sequencetool']], + 'dirs': ['alpha/%s' % d for d in ['data', 'lib', 'userdocs']] + + ['pyinclude', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["alpha -h"] + +modextrapaths = { + 'PATH': 'alpha', + 'PYTHONPATH': ['pyinclude', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' From bf13ec028d380dcd3904a573af67a93353c3cb90 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Mar 2020 01:18:36 +0200 Subject: [PATCH 018/431] networkx: add version 2.2 for Python 2 with foss/2019b --- .../networkx-2.2-foss-2019b-Python-2.7.16.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..d61e7b42be6 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', versionsuffix), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From bc052595fddbb22e15200cf36e04bd4e824380aa Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Mar 2020 00:33:47 +0100 Subject: [PATCH 019/431] Alpha: patch hardcoded email.txt --- .../a/Alpha/Alpha-20190607_fix-email.patch | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/Alpha/Alpha-20190607_fix-email.patch diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607_fix-email.patch b/easybuild/easyconfigs/a/Alpha/Alpha-20190607_fix-email.patch new file mode 100644 index 00000000000..9e8ad876470 --- /dev/null +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607_fix-email.patch @@ -0,0 +1,24 @@ +Remove hardcoded path to email.txt +author: Alex Domingo (Vrije Universiteit Brussel) +--- alpha/lib/email.py 2019-05-21 18:07:12.000000000 +0200 ++++ alpha/lib/email.py 2019-06-14 11:35:04.129371000 +0200 +@@ -1,10 +1,12 @@ + import os + THIS_FILE_DIR = os.path.dirname(os.path.realpath(__file__)) ++user_home_dir = os.path.expanduser("~") ++user_alpha_dir = os.path.join( user_home_dir, ".alpha") + + import sys + + +-def getEmail(filename=THIS_FILE_DIR+'/email.txt'): ++def getEmail(filename=user_alpha_dir+'/email.txt'): + """ + Read an email address from the file. + """ +@@ -18,4 +20,4 @@ + else: + sys.exit('ERROR: email "{}" format unrecognized.'.format(email)) + +- sys.exit('ERROR: please put your email address in "lib/email.txt".') ++ sys.exit('ERROR: please put your email address in: ' + user_alpha_dir + '/email.txt') From 77037f2bf08b24142c53654cba03cb15cdf455f9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Mar 2020 00:51:46 +0100 Subject: [PATCH 020/431] Alpha: downgrade matplotlib to version 2.2.4 --- .../a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb index a4bf824daae..9669d22a843 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -18,7 +18,7 @@ dependencies = [ ('Clustal-Omega', '1.2.4'), ('GenomeTools', '1.6.1'), ('GTK+', '3.24.13'), - ('matplotlib', '2.2.5', versionsuffix), + ('matplotlib', '2.2.4', versionsuffix), ('networkx', '2.2', versionsuffix), ('pydot', '1.4.1'), ('PyGObject', '3.34.0', versionsuffix), From ecdb0d9a6563d33867a377f9a063c7c743e21e1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Mar 2020 11:12:10 +0100 Subject: [PATCH 021/431] adding easyconfigs: NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb --- .../NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0d2d255e29f --- /dev/null +++ b/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NLMpy' +version = '0.1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.org/project/nlmpy' +description = """NLMpy is a Python package for the creation of neutral landscape models that are widely used + in the modelling of ecological patterns and processes across landscapes.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['618eebc22a9fd8268893eaab14d40a2dd16939f31d59d00c46b6c1fc03e5b6d0'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From a96cae08d9a591a4fc58035375aacbf013c9b01f Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 10 Mar 2020 17:02:30 +0200 Subject: [PATCH 022/431] adding easyconfigs: metaerg-1.2.3-intel-2019b-Python-2.7.16.eb, ARAGORN-1.2.38-GCCcore-8.3.0.eb, Bio-EUtilities-1.76-GCCcore-8.3.0.eb, LWP-Protocol-https-6.07-GCCcore-8.3.0.eb, MinPath-1.4-intel-2019b-Python-2.7.16.eb, MinCED-0.4.2-GCCcore-8.3.0.eb --- .../a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb | 39 ++++++++ .../Bio-EUtilities-1.76-GCCcore-8.3.0.eb | 88 +++++++++++++++++++ .../LWP-Protocol-https-6.07-GCCcore-8.3.0.eb | 72 +++++++++++++++ .../m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb | 32 +++++++ .../MinPath-1.4-intel-2019b-Python-2.7.16.eb | 45 ++++++++++ ...metaerg-1.2.3-intel-2019b-Python-2.7.16.eb | 64 ++++++++++++++ 6 files changed, 340 insertions(+) create mode 100644 easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb create mode 100644 easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..c76c4617cde --- /dev/null +++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'ARAGORN' +version = '1.2.38' + +# HTTPS not working +homepage = 'http://mbio-serv2.mbioekol.lu.se/ARAGORN/' +description = "a program to detect tRNA genes and tmRNA genes in nucleotide sequences" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['4b84e3397755fb22cc931c0e7b9d50eaba2a680df854d7a35db46a13cecb2126'] + +cmds_map = [ + (".*", "$CC $CFLAGS -o aragorn aragorn%(version)s.c") +] + +files_to_copy = [ + (['aragorn'], 'bin'), + (['aragorn.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/aragorn'], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + 'aragorn --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..341ac8926c7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb @@ -0,0 +1,88 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Bundle' + +name = 'Bio-EUtilities' +version = '1.76' + +homepage = 'https://github.com/bioperl/bio-eutilities' +description = "BioPerl low-level API for retrieving and storing data from NCBI eUtils" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] +dependencies = [ + ('Perl', '5.30.0'), + ('BioPerl', '1.7.2'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::MakeMaker', '7.44', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.44.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['52a18f8271250faf5f3527499dd2b78d3b4fd3b064408d0cfdda9a3538887188'], + }), + ('IO::Handle', '1.42', { + 'source_tmpl': 'IO-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('Test::More', '0', { + 'source_tmpl': 'Test-Simple-1.302171.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], + }), + ('Bio::ASN1::EntrezGene', '1.73', { + 'source_tmpl': 'Bio-ASN1-EntrezGene-1.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': ['f9e778db705ce5c35ad2798e38a8490b644edfdc14253aa1b74a1f5e79fc6a4b'], + }), + ('Cwd', '3.75', { + 'source_tmpl': 'PathTools-3.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('Data::Dumper', '2.173', { + 'source_tmpl': 'Data-Dumper-2.173.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + }), + ('LWP::UserAgent', '6.06', { + 'source_tmpl': 'libwww-perl-6.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], + }), + ('Text::Wrap', '2013.0523', { + 'source_tmpl': 'Text-Tabs+Wrap-2013.0523.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MU/MUIR/modules'], + 'checksums': ['b9cb056fffb737b9c12862099b952bf4ab4b1f599fd34935356ae57dab6f655f'], + }), + ('base', '2.23', { + 'source_tmpl': 'base-2.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['40f55841299a9fe6fab03cd098f94e9221fb516978e9ef40fd8ff2cbd6625dde'], + }), + ('Bio::DB::EUtilities', version, { + 'source_tmpl': 'Bio-EUtilities-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + 'checksums': ['dbdd913e60cd48f0a5a03ca6b05b424eb2a644495ea0cbe432be9fe3fada4fed'], + }), +] + +# Need to run tests after install to get perl modules on perl path. +sanity_check_commands = ["cd %(builddir)s/BioDBEUtilities/Bio-EUtilities-1.76 && make test"] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..c9d5062e915 --- /dev/null +++ b/easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb @@ -0,0 +1,72 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Bundle' + +name = 'LWP-Protocol-https' +version = '6.07' + +homepage = 'https://github.com/libwww-perl/lwp-protocol-https' +description = "Provide https support for LWP::UserAgent" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] +dependencies = [ + ('Perl', '5.30.0'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('LWP::UserAgent', '6.06', { + 'source_tmpl': 'libwww-perl-6.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], + }), + ('Mozilla::CA', '20110101', { + 'source_tmpl': 'Mozilla-CA-20180117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], + 'checksums': ['f2cc9fbe119f756313f321e0d9f1fac0859f8f154ac9d75b1a264c1afdf4e406'], + }), + ('Net::HTTPS', '6', { + 'source_tmpl': 'Net-HTTP-6.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['52b76ec13959522cae64d965f15da3d99dcb445eddd85d2ce4e4f4df385b2fc4'], + }), + ('Net::HTTPS', '6', { + 'source_tmpl': 'Net-HTTP-6.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['52b76ec13959522cae64d965f15da3d99dcb445eddd85d2ce4e4f4df385b2fc4'], + }), + ('Test::More', '0', { + 'source_tmpl': 'Test-Simple-1.302171.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], + }), + ('Test::RequiresInternet', '0', { + 'source_tmpl': 'Test-RequiresInternet-0.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN/'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('LWP::Protocol::https', version, { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['522cc946cf84a1776304a5737a54b8822ec9e79b264d0ba0722a70473dbfb9e7'], + }), +] + +# Need to run tests after install to get perl modules on perl path. +sanity_check_commands = ["cd %(builddir)s/LWPProtocolhttps/LWP-Protocol-https-6.07 && make test"] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..f1caaabeab5 --- /dev/null +++ b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb @@ -0,0 +1,32 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'MinCED' +version = '0.4.2' + +homepage = 'https://github.com/ctSkennerton/minced' +description = """Mining CRISPRs in Environmental Datasets""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +# https://github.com/ctSkennerton/minced +github_account = 'ctSkennerton' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['35b6ee22fe6bdc26a31d0203a7dcc6bd1a19fd6733c60d80ceb44431884af165'] + +dependencies = [('Java', '11', '', True)] + +# minced executable has to be in the same directory as jar +files_to_copy = [(['minced', 'minced.jar'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/minced.jar', 'bin/minced'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['minced --version'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..7620483174e --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'MinPath' +version = '1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://omics.informatics.indiana.edu/MinPath' +description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions + using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological + pathways for a query dataset.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://omics.informatics.indiana.edu/mg/get.php?justdoit=yes&software='] +sources = ['minpath%(version)s.tar.gz'] +patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] +checksums = [ + '665e90b5ee7fa5837d13b1145cdf3eafa691d25c1ce4bb76847dfa771ff24551', # minpath1.4.tar.gz + '35ac9d18ec5e2d6e2345de708236ed12cddcccbd8fc0c5a3652ecd838dc57822', # MinPath-1.4_fix-glpsol-path.patch +] + +dependencies = [ + ('Python', '2.7.16'), + ('GLPK', '4.65'), +] + +# remove included old GLPK copy +postinstallcmds = ["rm -rf %(installdir)s/glpk-*"] + +sanity_check_paths = { + 'files': ['MinPath%(version)s.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "MinPath%(version)s.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "MinPath%(version)s.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "MinPath%(version)s.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", +] + +modextrapaths = {'PATH': ''} + +modextravars = {'MinPath': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..c36326b9103 --- /dev/null +++ b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb @@ -0,0 +1,64 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# NOTE: Operating MetaErg requires reference DB, see: +# https://github.com/xiaoli-dong/metaerg#metaerg-reference-db + + +easyblock = 'Tarball' + +name = 'metaerg' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/xiaoli-dong/metaerg' +description = """MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +github_account = 'xiaoli-dong' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['dbe8ebc29ff8464d00f8a90f4dd9e48eaaadb3e6a95cbf7c620cac4f9d6c8c3c'] + +dependencies = [ + ('Python', '2.7.16'), + ('Perl', '5.30.0'), + ('BioPerl', '1.7.2'), + ('BLAST+', '2.9.0'), + ('ARAGORN', '1.2.38'), + ('DIAMOND', '0.9.30'), + ('HMMER', '3.2.1'), + ('MinPath', '1.4', versionsuffix), + ('prodigal', '2.6.3'), + ('MinCED', '0.4.2'), + ('Bio-EUtilities', '1.76'), + ('LWP-Protocol-https', '6.07'), + ('swissknife', '1.79'), +] + +modextrapaths = { + 'PERL5LIB': ['lib/perl5/site_perl/%(perlver)s/'], +} + +local_bin_files = [ + 'add_binid2cds.pl', 'annotCDs.pl', 'filterContigByLength.pl', 'getVizBinInput.pl', + 'metaerg.pl', 'output_sunburst_json.abund.pl', 'predictFeatures.pl', 'search_parser.pl', + 'setup_rnahmm_db.pl', 'util.pl', 'add_binid2master_dot_tsv.pl', 'check_tools.pl', + 'getHMMs.pl', 'gff2geneAnnot.pl', 'output_reports.pl', 'output_sunburst_json.pl', + 'rna2taxon.pl', 'setup_db_kegg_enzyme.pl', 'split_GoodBad_bins.pl', + 'add_lineage_to_checkm_tree.pl', 'fastaContig2Gff.pl', 'getSeqs.pl', 'gff2profiles.pl', + 'output_sunburst_json.abund.org.pl', 'output_tree_json.pl', 'rRNAFinder.pl', + 'setup_db.pl', 'split_hmm.pl', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['metaerg.sql'], + 'dirs': ['bin', 'docs', 'example', 'hmmrna', 'template', 'txt'], +} + +sanity_check_commands = [ + 'metaerg.pl --version' +] + +moduleclass = 'bio' From 6ba147542fed6c849207847f8b37e0a5ae140cfa Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 10 Mar 2020 17:08:26 +0200 Subject: [PATCH 023/431] minor fixes --- .../b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb | 2 +- .../m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb index 341ac8926c7..5cf24ec9c01 100644 --- a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb @@ -85,4 +85,4 @@ sanity_check_paths = { 'dirs': ['lib/perl5/site_perl/%(perlver)s/'], } -moduleclass = 'data' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb index f1caaabeab5..838cdb693bc 100644 --- a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb @@ -29,4 +29,4 @@ sanity_check_paths = { sanity_check_commands = ['minced --version'] -moduleclass = 'math' +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb index c36326b9103..55dd840b1e1 100644 --- a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb @@ -4,7 +4,6 @@ # NOTE: Operating MetaErg requires reference DB, see: # https://github.com/xiaoli-dong/metaerg#metaerg-reference-db - easyblock = 'Tarball' name = 'metaerg' From f931eba30ebf8d97d028d8199165495a42cbe1ec Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 12 Mar 2020 17:10:01 +0200 Subject: [PATCH 024/431] Alpha: use final_dir from tarball easyblock --- ...Alpha-20190607-foss-2019b-Python-2.7.16.eb | 42 +++++++++---------- 1 file changed, 20 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb index 9669d22a843..f71d253537e 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -1,8 +1,9 @@ easyblock = 'Bundle' name = 'Alpha' -local_commit = 'e027eb0fea1e' version = '20190607' +local_alpha_commit = 'e027eb0fea1e' +local_pyinc_commit = '0f8a00b8c10c' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.lirmm.fr/~swenson/alpha/alpha.htm' @@ -27,43 +28,40 @@ dependencies = [ ] components = [ - ('pyinclude', '0f8a00b8c10c', { + ('progressbar', '2.5', { + 'easyblock': 'PythonPackage', + 'source_urls': [PYPI_SOURCE], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['5d81cb529da2e223b53962afd6c8ca0f05c6670e40309a7219eacc36af9b6c63'], + 'start_dir': '%(name)s-%(version)s', + }), + ('pyinclude', '20190223', { 'easyblock': 'Tarball', 'source_urls': ['https://bitbucket.org/thekswenson/%(name)s/get/'], - 'sources': [{ - 'download_filename': '%(version)s.zip', - 'filename': '%(name)s-%(version)s.zip', - 'extract_cmd': "unzip %s && mv thekswenson-%(name)s-%(version)s %(name)s" - }], + 'sources': [{'download_filename': '%s.zip' % local_pyinc_commit, 'filename': '%(name)s-%(version)s.zip'}], 'checksums': ['9dc9b2bafbfe7a694ff4025164dc6e356989ee89b914691457fb0a474fe66c9e'], + 'start_dir': 'thekswenson-%%(name)s-%s' % local_pyinc_commit, + 'final_dir': '%(name)s', }), - (name, local_commit, { + (name, version, { 'easyblock': 'Tarball', 'source_urls': ['https://bitbucket.org/thekswenson/%(namelower)s/get/'], - 'sources': [{ - 'download_filename': '%(version)s.zip', - 'filename': '%(namelower)s-%(version)s.zip', - 'extract_cmd': "unzip %s && mv thekswenson-%(namelower)s-%(version)s %(namelower)s" - }], + 'sources': [{'download_filename': '%s.zip' % local_alpha_commit, 'filename': '%(namelower)s-%(version)s.zip'}], 'patches': ['%s-%s_fix-email.patch' % (name, version)], 'checksums': [ 'a9a0857ee080864c0d187f1f537aebdb3a61e58dd555b97dffbf2c2d73465f2a', # alpha-e027eb0fea1e.zip '342d5d37bcfc19a2487c3b08860adc4246736919948b1968f899b0c595d7125d', # Alpha-20190607_fix-email.patch ], - }), - # PythonPackage is last to not have its source copied by Tarball blocks - ('progressbar', '2.5', { - 'easyblock': 'PythonPackage', - 'source_urls': [PYPI_SOURCE], - 'sources': ['%(name)s-%(version)s.tar.gz'], - 'checksums': ['5d81cb529da2e223b53962afd6c8ca0f05c6670e40309a7219eacc36af9b6c63'], - 'start_dir': '%(name)s-%(version)s', + 'start_dir': 'thekswenson-%%(namelower)s-%s' % local_alpha_commit, + 'final_dir': '%(namelower)s', + 'keepsymlinks': True, }), ] +local_arch = 'OSX' if SHLIB_EXT == 'dylib' else 'x86_64' postinstallcmds = [ 'ln -s ${EBROOTGENOMETOOLS} %(installdir)s/%(namelower)s/lib/gtdir', - 'cd %(installdir)s/%(namelower)s/lib/ccode && ln -s bin_x86_64/eqclasses.so eqclasses.so', + 'cd %%(installdir)s/%%(namelower)s/lib/ccode && ln -s bin_%s/eqclasses.so eqclasses.so' % local_arch, ] sanity_check_paths = { From d2e6e34289b84ddbbd61ca166a1b75d9f4f4c4f5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 12 Mar 2020 17:15:32 +0200 Subject: [PATCH 025/431] Alpha: add sanity check for eqclasses.so --- .../a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb index f71d253537e..b7c944f92f4 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -61,11 +61,13 @@ components = [ local_arch = 'OSX' if SHLIB_EXT == 'dylib' else 'x86_64' postinstallcmds = [ 'ln -s ${EBROOTGENOMETOOLS} %(installdir)s/%(namelower)s/lib/gtdir', + # Alpha provides eqclasses.so for both Linux and OS X 'cd %%(installdir)s/%%(namelower)s/lib/ccode && ln -s bin_%s/eqclasses.so eqclasses.so' % local_arch, ] sanity_check_paths = { - 'files': ['alpha/%s' % x for x in ['alpha', 'analyzeblocks', 'sequencetool']], + 'files': ['alpha/%s' % x for x in ['alpha', 'analyzeblocks', 'sequencetool']] + + ['alpha/lib/ccode/eqclasses.so'], 'dirs': ['alpha/%s' % d for d in ['data', 'lib', 'userdocs']] + ['pyinclude', 'lib/python%(pyshortver)s/site-packages'], } From 4b8ca87a7c8ea0f77044adbf1abc7c6866ec358b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 13 Mar 2020 16:02:21 +0200 Subject: [PATCH 026/431] Alpha: use OS_TYPE to set local_arch --- .../a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb index b7c944f92f4..eb6939a4552 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -58,7 +58,7 @@ components = [ }), ] -local_arch = 'OSX' if SHLIB_EXT == 'dylib' else 'x86_64' +local_arch = {'Darwin': 'OSX', 'Linux': 'x86_64'}[OS_TYPE] postinstallcmds = [ 'ln -s ${EBROOTGENOMETOOLS} %(installdir)s/%(namelower)s/lib/gtdir', # Alpha provides eqclasses.so for both Linux and OS X From d7d8285725ab31887cbdc9ff8a76f5db3387e1b7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 13 Mar 2020 16:07:43 +0200 Subject: [PATCH 027/431] adding easyconfigs: BBMap-38.79-GCC-8.3.0.eb --- .../b/BBMap/BBMap-38.79-GCC-8.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb new file mode 100644 index 00000000000..90bb802ed78 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.79' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['72891105b6d3e190b5b1d60fb964077a997cf5d2647c472b213a6dd46e1ca07c'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From 322620ff4a67d45fea6cf77a40f0024f3c72baba Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 16 Mar 2020 13:49:01 +0200 Subject: [PATCH 028/431] adding easyconfigs: NGS-2.10.4-GCCcore-8.3.0.eb, ncbi-vdb-2.10.4-gompi-2019b.eb, SRA-Toolkit-2.10.4-gompi-2019b.eb, NGS-Python-2.10.4-gompi-2019b-Python-2.7.16.eb and patches: NGS-Python-2.10.4_fix-prefix.patch --- ...Python-2.10.4-gompi-2019b-Python-2.7.16.eb | 43 ++++++++++ .../NGS-Python-2.10.4_fix-prefix.patch | 22 +++++ .../n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb | 46 ++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.10.4-gompi-2019b.eb | 44 ++++++++++ .../SRA-Toolkit-2.10.4-gompi-2019b.eb | 85 +++++++++++++++++++ 5 files changed, 240 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4-gompi-2019b-Python-2.7.16.eb create mode 100644 easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4_fix-prefix.patch create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.4-gompi-2019b.eb create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.4-gompi-2019b.eb diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4-gompi-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4-gompi-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..706e61677c1 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4-gompi-2019b-Python-2.7.16.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'NGS-Python' +version = '2.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +source_urls = ['https://github.com/ncbi/ngs/archive'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['NGS-Python-%(version)s_fix-prefix.patch'] +checksums = [ + '6f5db2269c6afc8e51a50fbcab9c63f4b1d6b69e483c6acb40d8f9e52f8282b1', # NGS-Python-2.10.4.tar.gz + '3be6283af5354f157dbece7ce8b694362e9083781b02b2355f74f4f09996e328', # NGS-Python-2.10.4_fix-prefix.patch +] + +builddependencies = [('Perl', '5.30.0')] + +dependencies = [ + ('Python', '2.7.16'), + ('NGS', version, '-Java-11'), + ('ncbi-vdb', version), +] + +start_dir = '%(namelower)s' + +# Change default build directory and add paths to dependencies in EB +configopts = '--build-prefix=%(builddir)s --with-ngs-sdk-prefix=$EBROOTNGS --with-ncbi-vdb-prefix=$EBROOTNCBIMINVDB' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python2.7/site-packages', 'share/examples-python'], +} + +sanity_check_commands = [('python', "-c 'import ngs'")] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4_fix-prefix.patch b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4_fix-prefix.patch new file mode 100644 index 00000000000..15f19c577dc --- /dev/null +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.10.4_fix-prefix.patch @@ -0,0 +1,22 @@ +correctly specify prefix to install NGS-Python +author: Kenneth Hoste (HPC-UGent), Alex Domingo (Vrije Universiteit Brussel) +--- ngs-python/Makefile.python.orig 2020-03-16 12:31:56.476725000 +0100 ++++ ngs-python/Makefile.python 2020-03-16 12:32:57.524391000 +0100 +@@ -60,7 +60,7 @@ + + else + @ echo "Installing ngs-python package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + endif + +@@ -85,7 +85,7 @@ + + else + @ echo "Installing ngs package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + + ifneq (, $(NGS_LIBDIR)) diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb new file mode 100644 index 00000000000..bf41fbf66b7 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb @@ -0,0 +1,46 @@ +easyblock = 'Bundle' + +name = 'NGS' +version = '2.10.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [ + ('binutils', '2.32'), + ('Perl', '5.30.0'), +] + +dependencies = [('Java', '11', '', True)] + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://github.com/ncbi/ngs/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['6f5db2269c6afc8e51a50fbcab9c63f4b1d6b69e483c6acb40d8f9e52f8282b1'], +} + +components = [ + ('NGS-SDK', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), + ('NGS-Java', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), +] + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.4-gompi-2019b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.4-gompi-2019b.eb new file mode 100644 index 00000000000..c3cc10ba0b6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.4-gompi-2019b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.10.4' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['b78d574b1b20c4b864a0358e0660481497fc1b269f9bee621b4aa7866d81dfb7'] + +builddependencies = [('Perl', '5.30.0')] + +dependencies = [ + ('NGS', version, '-Java-11'), + ('file', '5.38'), # provides libmagic + ('HDF5', '1.10.5'), + ('libxml2', '2.9.9'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.4-gompi-2019b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.4-gompi-2019b.eb new file mode 100644 index 00000000000..30d75d3da7e --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.4-gompi-2019b.eb @@ -0,0 +1,85 @@ +easyblock = 'Bundle' + +name = 'SRA-Toolkit' +version = '2.10.4' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2019b'} + +builddependencies = [('Perl', '5.30.0')] + +dependencies = [ + ('NGS', version, '-Java-11'), + ('file', '5.38'), # provides libmagic + ('HDF5', '1.10.5'), + ('libxml2', '2.9.9'), +] + +# Add addtional libraries needed to statically link HDF5 from EB +local_base_preconfig = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl && " + +# Change default build directory and add paths to dependencies in EB +local_base_config = '--build-prefix=%(builddir)s --with-ngs-sdk-prefix=$EBROOTNGS ' +local_base_config += '--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2' +local_vdb_config = local_base_config + ' --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar' +# SRA-Tools need the source and build directory of NCBI-VDB +local_sra_config = local_base_config + ' --with-ncbi-vdb-sources=%(builddir)s/ncbi-vdb-%(version)s' +local_sra_config += ' --with-ncbi-vdb-build=%(builddir)s/ncbi-vdb ' + +# Replace hardcoded optimization flags with flags from EB +local_base_prebuild = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && " +local_base_prebuild += 'EBFLAGS="$CFLAGS" ' +local_base_preinstall = 'EBFLAGS="$CFLAGS" ' + +# Standalone compilation of utf8proc to ensure that its shared objects are available +local_sra_prebuild = "make -C tools/driver-tool/utf8proc && " +# Add addtional libraries needed to statically link HDF5 from EB +local_sra_prebuild += "sed -i 's/-sm/-sm -lmpi -lsz/' tools/pacbio-load/Makefile && " +# Add additional libraries needed to statically link libxml2 from EB +local_sra_prebuild += "find build/ -name \"ld*.sh\" -exec sed -i 's/-lxml2/-lxml2 -lz -llzma/g' {} + && " +local_sra_prebuild += local_base_prebuild + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'start_dir': '%(namelower)s-%(version)s', + 'preconfigopts': local_base_preconfig, + 'preinstallopts': local_base_preinstall, +} + +components = [ + # NCBI-VDB has to be installed as component instead of dependency because SRA-Tools needs its sources + ('NCBI-VDB', version, { + 'checksums': ['b78d574b1b20c4b864a0358e0660481497fc1b269f9bee621b4aa7866d81dfb7'], + 'configopts': local_vdb_config, + 'prebuildopts': local_base_prebuild, + }), + ('SRA-Tools', version, { + 'checksums': ['7a65203421d81f4c4f61eff13bc965f4ef1a7231cedc02005e4ae3b886520441'], + 'configopts': local_sra_config, + 'prebuildopts': local_sra_prebuild, + }), +] + +local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', + 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'kget', + 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', + 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', + 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', + 'vdb-validate'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin] + + ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [] +} + +moduleclass = 'bio' From f9e5d6c3283d719b7b841a3daa95f952d78425c4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 16 Mar 2020 14:01:10 +0200 Subject: [PATCH 029/431] file: add version 5.38 with GCCcore/8.3.0 --- .../f/file/file-5.38-GCCcore-8.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.38-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.38-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/file/file-5.38-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..9d5d6003f59 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.38-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.38' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['593c2ffc2ab349c5aea0f55fedfe4d681737b6b62376a9b3ad1e77b2cc19fa34'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.32'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From a9ad9a5b8cff422b0d59eb2f429bbd926f45f914 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Mar 2020 16:10:51 +0200 Subject: [PATCH 030/431] adding easyconfigs: FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb --- ...onCatcher-1.20-foss-2019b-Python-2.7.16.eb | 110 ++++++++++++++++++ 1 file changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..4c2dc45f594 --- /dev/null +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,110 @@ +easyblock = 'Bundle' + +name = 'FusionCatcher' +version = '1.20' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ndaniel/fusioncatcher' +description = """FusionCatcher searches for novel/known somatic fusion genes, translocations, +and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS +platforms like Solexa/HiSeq/NextSeq/MiSeq/MiniSeq) from diseased samples.""" +github_account = 'ndaniel' + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Java', '11', '', True), + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('BLAT', '3.5'), + ('Bowtie', '1.2.3'), + ('Bowtie2', '2.3.5.1'), + ('BWA', '0.7.17'), + ('Kent_tools', '20190326', '-linux.x86_64', True), + ('SRA-Toolkit', '2.10.4'), + ('STAR', '2.7.2b'), + ('picard', '2.21.6', '-Java-11', True), # Optional + ('Velvet', '1.2.10', '-mt-kmer_191'), # Optional + ('OpenPyXL', '2.6.4'), # Optional + ('parallel', '20190922'), # Optional + ('pigz', '2.4'), + ('zlib', '1.2.11'), +] + +local_bbmap_makefile = 'makefile.%s' % {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_SOURCE], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['4c66dbd7be64aaf52ab1f02278f06d9a8082b7f3f30a8045a50b4899e22a0385'], + 'start_dir': '%(namelower)s-%(version)s', + }), + # FusionCatcher requires a fork of seqtk with features not available upstream + ('seqtk', '1.2-r101c', { + 'easyblock': 'MakeCp', + 'source_urls': ['http://github.com/ndaniel/seqtk/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['4a57fbe828eccaa4f0122c84bf9c4c5409a024ad9deace31ec7bee6d25cf5e49'], + 'start_dir': '%(name)s-%(version)s', + 'files_to_copy': [(['seqtk'], 'tools/%(name)s')], + }), + # FusionCatcher requires this very specific version of BBMap + ('BBMap', '38.44', { + 'easyblock': 'MakeCp', + 'source_urls': [SOURCEFORGE_SOURCE], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['63ecdc83cdb0aaf5106b919df487f50a6b65e816d990501e9f74704c04b2a84a'], + 'start_dir': '%(namelower)s', + 'prebuildopts': "cd jni && ", + 'buildopts': "-f %s" % local_bbmap_makefile, + 'files_to_copy': [(['*'], 'tools/%(namelower)s')], + }), +] + +# Set paths in the configuration file +postinstallcmds = [ + 'sed -i "s|python = /usr/bin/|python = $EBROOTPYTHON/bin/|g" %(installdir)s/etc/configuration.cfg', + 'sed -i "s|java = /usr/bin/|python = $EBROOTJAVA/bin/|g" %(installdir)s/etc/configuration.cfg', + 'sed -i "s|paralell/src|parallel/bin|g" %(installdir)s/etc/configuration.cfg', +] + +# Create symlinks in installation dir to dependencies from EB +postinstallcmds += [ + 'ln -s $EBROOT%s %%(installdir)s/tools/%s' % (d, d.lower()) for d in [ + 'BLAT', 'BOWTIE', 'BOWTIE2', 'BWA', 'PARALLEL', 'PICARD', 'PIGZ', 'STAR', 'VELVET' + ] +] +postinstallcmds += [ + 'ln -s $EBROOT%s %%(installdir)s/tools/%s' % d for d in [ + ('KENT_TOOLS/bin', 'liftover'), + ('SRAMINTOOLKIT', 'sratoolkit'), + ('BIOPYTHON/lib/python%(pyshortver)s/site-packages/Bio', 'biopython'), + ('SCIPYMINBUNDLE/lib/python%(pyshortver)s/site-packages/numpy', 'numpy'), + ('OPENPYXL/lib/python%(pyshortver)s/site-packages/openpyxl', 'openpyxl'), + ('PYTHON/lib/python%(pyshortver)s/site-packages/xlrd', 'xlrd'), + ] +] + +# Link the required Ensembl database +# Database can be created after install with `fusioncatcher-build -g homo_sapiens -o /path/to/human_v98` +# More information at https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md +# postinstallcmds += [ +# 'ln -s /path/to/database/human_v98 %(installdir)s/data/human_v98', +# 'cd %(installdir)s/data && ln -s human_v98 current', +# ] + +# Tests need 16 cores and 64 GB of RAM as well as the Ensembl database +# postinstallcmds += ['%(installdir)s/test/test.sh'] + +sanity_check_paths = { + 'files': ['bin/fusioncatcher', 'bin/fusioncatcher-batch', 'bin/fusioncatcher-build', 'etc/configuration.cfg', + 'tools/seqtk/seqtk', 'tools/bbmap/bbmap.sh', 'tools/bbmap/jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': ['data', 'test'], +} + +sanity_check_commands = ["fusioncatcher --help"] + +moduleclass = 'bio' From d9343bf4bca70aad502d0d314e64e3f07b2d4aff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2020 18:03:00 +0100 Subject: [PATCH 031/431] adding easyconfigs: HDDM-0.7.5-intel-2019b-Python-3.7.4.eb --- .../HDDM-0.7.5-intel-2019b-Python-3.7.4.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..6ce2f26eb3b --- /dev/null +++ b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'HDDM' +version = '0.7.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ski.clps.brown.edu/hddm_docs' +description = """HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation + of the Drift Diffusion Model (via PyMC).""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.7.4'), + ('matplotlib', '3.1.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('pymc', '2.3.7', { + 'patches': ['pymc-%(version)s_rename-await.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pymc-devs/pymc/archive/'], + 'checksums': [ + '12765987a5d64eaf210b1a32053990a0a4cacf2458e93d9b35ebab239032a4b5', # v2.3.7.tar.gz + 'cf46c4b7d68ef26f0b9b6c329f3939ed6c0911e1f304f08cbcf6b9d4c4c4df5f', # pymc-2.3.7_rename-await.patch + ], + }), + ('kabuki', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kabuki'], + 'checksums': ['3d5e727529b323b3f12ec583c05702e863e7d4b1f31a7ba6077058115eb066b1'], + }), + ('patsy', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/H/HDDM'], + 'checksums': ['da13c51db24816d77ee04ebe9f7adbe5e4304da8e11a58371c660477f80b7f99'], + }), +] + +sanity_check_paths = { + 'files': ['bin/hddm_demo.py'], + 'dirs': [], +} + +moduleclass = 'bio' From 4bc84be7ed994e4362f5609f4f97b800ce46b251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2020 18:03:57 +0100 Subject: [PATCH 032/431] add pymc patch required by HDDM 0.7.5 --- .../h/HDDM/pymc-2.3.7_rename-await.patch | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDDM/pymc-2.3.7_rename-await.patch diff --git a/easybuild/easyconfigs/h/HDDM/pymc-2.3.7_rename-await.patch b/easybuild/easyconfigs/h/HDDM/pymc-2.3.7_rename-await.patch new file mode 100644 index 00000000000..7c0e0d5a4b9 --- /dev/null +++ b/easybuild/easyconfigs/h/HDDM/pymc-2.3.7_rename-await.patch @@ -0,0 +1,23 @@ +await is a keyword in Python 3.7+, so rename 'await' method to avoid SyntaxError +see also https://github.com/pymc-devs/pymc/issues/188 +author: Kenneth Hoste (HPC-UGent) +--- pymc-2.3.7/pymc/threadpool.py.orig 2020-03-19 17:48:14.572211381 +0100 ++++ pymc-2.3.7/pymc/threadpool.py 2020-03-19 17:49:39.573111182 +0100 +@@ -343,7 +343,7 @@ + self.main_lock.release() + self.counter_lock.release() + +- def await(self): ++ def waitforit(self): + self.main_lock.acquire() + self.main_lock.release() + +@@ -384,7 +384,7 @@ + exc_callback=eb, + args=args, + requestID=id(args))) +- done_lock.await() ++ done_lock.waitforit() + + if exceptions: + six.reraise(*exceptions[0]) From b7c8c8d3ee2f29a5c470af7fb9d00af6d9bf6716 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Mar 2020 19:20:31 +0100 Subject: [PATCH 033/431] enable sanity_pip_check + make sure pymc patch file is found by tests --- .../easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb index 6ce2f26eb3b..686a59fa8c4 100644 --- a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb @@ -20,7 +20,7 @@ use_pip = True exts_list = [ ('pymc', '2.3.7', { - 'patches': ['pymc-%(version)s_rename-await.patch'], + 'patches': ['pymc-2.3.7_rename-await.patch'], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pymc-devs/pymc/archive/'], 'checksums': [ @@ -47,4 +47,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_pip_check = True + moduleclass = 'bio' From c90aed0f091e77c11ad977c224312b7968006d7c Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Mon, 23 Mar 2020 16:37:51 +0200 Subject: [PATCH 034/431] fixed issues, added missed swissknife easyblock --- .../a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb | 10 ++-- .../m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb | 1 + .../MinPath-1.4-intel-2019b-Python-2.7.16.eb | 2 +- .../swissknife-1.79-GCCcore-8.3.0.eb | 47 +++++++++++++++++++ 4 files changed, 53 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb index c76c4617cde..41b573c7cfd 100644 --- a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb @@ -18,9 +18,9 @@ source_urls = ['http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/'] sources = ['%(namelower)s%(version)s.tgz'] checksums = ['4b84e3397755fb22cc931c0e7b9d50eaba2a680df854d7a35db46a13cecb2126'] -cmds_map = [ - (".*", "$CC $CFLAGS -o aragorn aragorn%(version)s.c") -] +builddependencies = [('binutils', '2.32')] + +cmds_map = [(".*", "$CC $CFLAGS -o aragorn aragorn%(version)s.c")] files_to_copy = [ (['aragorn'], 'bin'), @@ -32,8 +32,6 @@ sanity_check_paths = { 'dirs': ['share/man'], } -sanity_check_commands = [ - 'aragorn --help' -] +sanity_check_commands = ['aragorn --help'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb index 838cdb693bc..9946faadc09 100644 --- a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb @@ -17,6 +17,7 @@ source_urls = [GITHUB_LOWER_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['35b6ee22fe6bdc26a31d0203a7dcc6bd1a19fd6733c60d80ceb44431884af165'] +builddependencies = [('binutils', '2.32')] dependencies = [('Java', '11', '', True)] # minced executable has to be in the same directory as jar diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb index 7620483174e..e3d6ac96da5 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2019b-Python-2.7.16.eb @@ -4,7 +4,7 @@ name = 'MinPath' version = '1.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://omics.informatics.indiana.edu/MinPath' +homepage = 'https://omics.informatics.indiana.edu/MinPath' description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.""" diff --git a/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0fef1d578f4 --- /dev/null +++ b/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Bundle' + +name = 'swissknife' +version = '1.79' + +homepage = 'https://sourceforge.net/projects/swissknife/' +description = "Perl module for reading and writing UniProtKB data in plain text format." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] +dependencies = [ + ('Perl', '5.30.0'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('Data::Dumper', '2.173', { + 'source_tmpl': 'Data-Dumper-2.173.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + }), + ('SWISS::Entry', version, { + 'source_tmpl': 'swissknife_%(version)s.tar.gz', + 'source_urls': [('https://sourceforge.net/projects/swissknife/files/swissknife/1.79', 'download')], + 'checksums': ['a7affa6ed892a8d9f4f9f1297d521076ac5bb1adfd85de5dc041679b53b949d6'], + }), +] + +# Need to run tests after install to get perl modules on perl path. +sanity_check_commands = ["cd %(builddir)s/SWISSEntry/swissknife_1.79 && make test"] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/'], +} + +moduleclass = 'data' From e4d6dd0207eb519248baa62572b577c5f808d1bc Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Mon, 23 Mar 2020 16:59:34 +0200 Subject: [PATCH 035/431] added Java versionsuffix --- ....2-GCCcore-8.3.0.eb => MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/m/MinCED/{MinCED-0.4.2-GCCcore-8.3.0.eb => MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb} (95%) diff --git a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb similarity index 95% rename from easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb index 9946faadc09..4cb42765502 100644 --- a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb @@ -5,6 +5,7 @@ easyblock = 'MakeCp' name = 'MinCED' version = '0.4.2' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/ctSkennerton/minced' description = """Mining CRISPRs in Environmental Datasets""" From 468fa27becaa443cdeb6f5d1e182d00d618ef964 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Mon, 23 Mar 2020 17:10:42 +0200 Subject: [PATCH 036/431] added Java versionsuffix for dependencies as well --- .../m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb index 55dd840b1e1..75d9f8c3d91 100644 --- a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb @@ -30,7 +30,7 @@ dependencies = [ ('HMMER', '3.2.1'), ('MinPath', '1.4', versionsuffix), ('prodigal', '2.6.3'), - ('MinCED', '0.4.2'), + ('MinCED', '0.4.2', '-Java-11'), ('Bio-EUtilities', '1.76'), ('LWP-Protocol-https', '6.07'), ('swissknife', '1.79'), From 124b23694e58419d0699ded15ba60c2dafbbee82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Mar 2020 19:09:54 +0100 Subject: [PATCH 037/431] {data}[intel/2020a] PyTables v3.6.1, numexpr v2.7.1 w/ Python 3.8.2 + LZO v2.10, Blosc 1.17.1 --- .../b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb | 28 +++++++++++ .../l/LZO/LZO-2.10-GCCcore-9.3.0.eb | 36 +++++++++++++++ .../numexpr-2.7.1-intel-2020a-Python-3.8.2.eb | 22 +++++++++ ...PyTables-3.6.1-intel-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 4 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c6a677dfb3f --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.17.1-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.17.1' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['19a6948b579c27e8ac440b4f077f99fc90e7292b1d9cb896bec0fd781d68fba2'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..54e56fb1519 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.34')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..63851a07ed5 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,22 @@ +name = 'numexpr' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c6ae3bb5688184b922b43fc47de49d642576d0feec55a1b679caa66efae90a1'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ab372ecd732 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('numexpr', '2.7.1', versionsuffix), + ('HDF5', '1.10.6'), + ('LZO', '2.10'), + ('Blosc', '1.17.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' From f483567d39a63a76489856ac338eb28296d25a53 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 29 Mar 2020 18:39:37 +0200 Subject: [PATCH 038/431] adding easyconfigs: GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb --- ...Python-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..369eff300c5 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gitpython-developers/GitPython' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('smmap', '3.0.1', { + 'checksums': ['171484fe62793e3626c8b05dd752eb2ca01854b0c55a1efc0dc4210fccb65446'], + }), + ('gitdb', '4.0.2', { + 'checksums': ['598e0096bb3175a0aab3a0b5aedaa18a9a25c6707e0eca0695ba1a0baf1b2150'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['e426c3b587bd58c482f0b7fe6145ff4ac7ae6c82673fc656f489719abca6f4cb'], + }), +] + +moduleclass = 'lib' From 324fe7607898e73e3ae83f62bf678be7b7a24d23 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Wed, 1 Apr 2020 11:11:06 +0200 Subject: [PATCH 039/431] adding easyconfigs: RMBlast-2.10.0-foss-2018b.eb --- .../r/RMBlast/RMBlast-2.10.0-foss-2018b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb new file mode 100644 index 00000000000..e537e661e80 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.10.0' + +homepage = 'http://www.repeatmasker.org/RMBlast.html' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/'] +sources = ['ncbi-blast-2.10.0+-src.tar.gz'] +patches = [ + ('http://www.repeatmasker.org/isb-2.10.0+-rmblast.patch.gz', 2) +] +checksums = [ + '3acdd9cec01c4f43e56aeaf89049cb8f8013d60b9c1705eced10166967f1d926', # ncbi-blast-2.10.0+-src.tar.gz + 'f17079292d137e73fa7bafac81e10d0be24ad8cbdd263f4baba8f93f25492bd6', # isb-2.10.0+-rmblast.patch.gz +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('Boost', '1.67.0'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt --without-krb5' +configopts += ' --without-openssl --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2' + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': ['lib', 'bin'] +} + +moduleclass = 'bio' From df9b88c7eb5851e08a18bebe991843795456fe49 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 1 Apr 2020 17:30:34 +0200 Subject: [PATCH 040/431] adding easyconfigs: rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb --- ...ioxarray-0.0.24-foss-2019b-Python-3.7.4.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..28a6c274b6d --- /dev/null +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.0.24-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'rioxarray' +version = '0.0.24' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/corteva/rioxarray' +description = "geospatial xarray extension powered by rasterio" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # rasterio depends on scipy + ('Pillow', '6.2.1'), + ('pyproj', '2.4.2', versionsuffix), + ('xarray', '0.15.1', versionsuffix), + ('GDAL', '3.0.2', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + ('cligj', '0.5.0', { + 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], + }), + ('click', '7.1.1', { + 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('s3transfer', '0.3.3', { + 'checksums': ['921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db'], + }), + ('jmespath', '0.9.5', { + 'checksums': ['cca55c8d153173e21baa59983015ad0daf603f9cb799904ff057bfb8ff8dc2d9'], + }), + ('botocore', '1.15.33', { + 'checksums': ['078a9731e054f9ee914a8eac77e445de3c1344a00d7eebfee9cae7f40b7f48e8'], + }), + ('boto3', '1.12.33', { + 'checksums': ['ad774b0e98d093ae425b85fdb25e5ae70a02ebe036c4222e1b93444699719221'], + }), + ('affine', '2.3.0', { + 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], + }), + ('rasterio', '1.1.3', { + 'checksums': ['fe2eac942ae4f8a97246c8cd3977723997817b53a9058cf1959551026c6177e7'], + }), + (name, version, { + 'checksums': ['f69acb5c935dee354da7a57f92528ef1464ec2ea0fdcdf2b0e4fe1c70b623c2c'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["rio --help"] + +moduleclass = 'data' From 355e3f7e2b30da958333abe9b80574a44e18feb6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 3 Apr 2020 12:31:59 +0200 Subject: [PATCH 041/431] adding easyconfigs: geopandas-0.7.0-foss-2019b-Python-3.7.4.eb --- ...geopandas-0.7.0-foss-2019b-Python-3.7.4.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..d0a0835848b --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'geopandas' +version = '0.7.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['19074b090ab928527193c50b383d31a259a9b84b18553562631295fa67f640bc'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('Shapely', '1.7.0', versionsuffix), + ('Fiona', '1.8.13', versionsuffix), + ('pyproj', '2.4.2', versionsuffix), +] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +moduleclass = 'geo' From 7ebf7bf73c4078677800ea9605d9ea51a060fa1e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 4 Apr 2020 01:24:21 +0200 Subject: [PATCH 042/431] add easyconfig and patch for RMBlast v2.9.0 based on BLAST+ --- .../r/RMBlast/BLAST+-2.9.0_fix_boost.patch | 96 +++++++++++++++++++ .../r/RMBlast/RMBlast-2.9.0-gompi-2019b.eb | 62 ++++++++++++ 2 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/BLAST+-2.9.0_fix_boost.patch create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.9.0-gompi-2019b.eb diff --git a/easybuild/easyconfigs/r/RMBlast/BLAST+-2.9.0_fix_boost.patch b/easybuild/easyconfigs/r/RMBlast/BLAST+-2.9.0_fix_boost.patch new file mode 100644 index 00000000000..8a41b1d193a --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/BLAST+-2.9.0_fix_boost.patch @@ -0,0 +1,96 @@ +Make changes necessary to work with Boost-1.70.0 +Without this patch it still works with Boost-1.67.0 +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur ncbi-blast-2.9.0+-src.orig/c++/include/corelib/test_boost.hpp ncbi-blast-2.9.0+-src/c++/include/corelib/test_boost.hpp +--- ncbi-blast-2.9.0+-src.orig/c++/include/corelib/test_boost.hpp 2018-09-17 16:00:14.000000000 +0200 ++++ ncbi-blast-2.9.0+-src/c++/include/corelib/test_boost.hpp 2019-05-24 19:54:52.702503781 +0200 +@@ -106,7 +106,7 @@ + " expected but not raised", \ + TL, CHECK_MSG, _ ); \ + } catch( E const& ex ) { \ +- ::boost::unit_test::ut_detail::ignore_unused_variable_warning( ex ); \ ++ ::boost::ignore_unused( ex ); \ + BOOST_TEST_TOOL_IMPL( 2, P, \ + "exception \"" BOOST_STRINGIZE( E ) \ + "\" raised as expected" postfix, \ +@@ -129,7 +129,7 @@ + " is expected", \ + TL, CHECK_MSG, _ ); \ + } catch( E const& ex ) { \ +- ::boost::unit_test::ut_detail::ignore_unused_variable_warning( ex ); \ ++ ::boost::ignore_unused( ex ); \ + BOOST_TEST_TOOL_IMPL( 2, P, prefix BOOST_STRINGIZE( E ) " is caught", \ + TL, CHECK_MSG, _ ); \ + } catch (...) { \ +@@ -168,7 +168,7 @@ + BOOST_CHECK_IMPL( false, "exception " BOOST_STRINGIZE( E ) \ + " is expected", TL, CHECK_MSG ); } \ + catch( E const& ex ) { \ +- boost::unit_test::ut_detail::ignore_unused_variable_warning( ex ); \ ++ boost::ignore_unused( ex ); \ + BOOST_CHECK_IMPL( P, prefix BOOST_STRINGIZE( E ) " is caught", \ + TL, CHECK_MSG ); \ + } \ +@@ -206,7 +206,7 @@ + + #ifdef BOOST_FIXTURE_TEST_CASE_NO_DECOR + # define NCBI_BOOST_DECORATOR_ARG \ +- , boost::unit_test::decorator::collector::instance() ++ , boost::unit_test::decorator::collector_t::instance() + #else + # define NCBI_BOOST_DECORATOR_ARG + #endif +@@ -785,7 +785,7 @@ + #ifdef BOOST_FIXTURE_TEST_CASE_WITH_DECOR + SNcbiTestRegistrar(boost::unit_test::test_case* tc, + unsigned int timeout, +- boost::unit_test::decorator::collector& decorator) ++ boost::unit_test::decorator::collector_t& decorator) + : TParent(tc, decorator) + { + tc->p_timeout.set(timeout); +diff -ur ncbi-blast-2.9.0+-src.orig/c++/src/corelib/teamcity_boost.cpp ncbi-blast-2.9.0+-src/c++/src/corelib/teamcity_boost.cpp +--- ncbi-blast-2.9.0+-src.orig/c++/src/corelib/teamcity_boost.cpp 2017-10-23 16:54:03.000000000 +0200 ++++ ncbi-blast-2.9.0+-src/c++/src/corelib/teamcity_boost.cpp 2019-05-24 16:50:56.825303031 +0200 +@@ -55,7 +55,7 @@ + + virtual void log_start(std::ostream&, boost::unit_test::counter_t test_cases_amount); + virtual void log_finish(std::ostream&); +- virtual void log_build_info(std::ostream&); ++ virtual void log_build_info(std::ostream&, bool log_build_info = true); + + virtual void test_unit_start(std::ostream&, boost::unit_test::test_unit const& tu); + virtual void test_unit_finish(std::ostream&, +@@ -135,7 +135,7 @@ + void TeamcityBoostLogFormatter::log_finish(std::ostream &/*out*/) + {} + +-void TeamcityBoostLogFormatter::log_build_info(std::ostream &/*out*/) ++void TeamcityBoostLogFormatter::log_build_info(std::ostream &/*out*/, bool log_build_info) + {} + + void TeamcityBoostLogFormatter::test_unit_start(std::ostream &out, boost::unit_test::test_unit const& tu) { +diff -ur ncbi-blast-2.9.0+-src.orig/c++/src/corelib/test_boost.cpp ncbi-blast-2.9.0+-src/c++/src/corelib/test_boost.cpp +--- ncbi-blast-2.9.0+-src.orig/c++/src/corelib/test_boost.cpp 2018-09-17 15:59:01.000000000 +0200 ++++ ncbi-blast-2.9.0+-src/c++/src/corelib/test_boost.cpp 2019-05-24 16:51:58.589513416 +0200 +@@ -248,7 +248,7 @@ + virtual + void log_finish (ostream& ostr); + virtual +- void log_build_info (ostream& ostr); ++ void log_build_info (ostream& ostr, bool log_build_info = true); + virtual + void test_unit_start (ostream& ostr, but::test_unit const& tu); + virtual +@@ -2086,9 +2086,9 @@ + } + + void +-CNcbiBoostLogger::log_build_info(ostream& ostr) ++CNcbiBoostLogger::log_build_info(ostream& ostr, bool log_build_info) + { +- m_Upper->log_build_info(ostr); ++ m_Upper->log_build_info(ostr, log_build_info); + } + + void diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.9.0-gompi-2019b.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.9.0-gompi-2019b.eb new file mode 100644 index 00000000000..6580d176772 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.9.0-gompi-2019b.eb @@ -0,0 +1,62 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.9.0' + +homepage = 'http://www.repeatmasker.org/RMBlast.html' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [ + 'BLAST+-%(version)s_fix_boost.patch', + ('http://www.repeatmasker.org/isb-%(version)s+-%(namelower)s-p2.patch.gz', 2), +] +checksums = [ + 'a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257', # ncbi-blast-2.9.0+-src.tar.gz + '44dc4a931896953d78c13097433ea6fc8d7990bd759c4e4e5bbb9b2574fb4154', # BLAST+-2.9.0_fix_boost.patch + '0d5cc11030a01f10cc413ce4f5a0f0cd91deb176a7a5559d3635881cd186cf9f', # isb-2.9.0+-rmblast-p2.patch.gz +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.43'), + ('Boost', '1.71.0'), + ('GMP', '6.1.2'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.3'), + ('LMDB', '0.9.24'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' From 0789f77f6f309b1d33838e40b98bee63eeeea584 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 4 Apr 2020 01:24:59 +0200 Subject: [PATCH 043/431] remove easyconfig RMBlast-2.10.0-foss-2018b.eb --- .../r/RMBlast/RMBlast-2.10.0-foss-2018b.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb deleted file mode 100644 index e537e661e80..00000000000 --- a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.10.0-foss-2018b.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'RMBlast' -version = '2.10.0' - -homepage = 'http://www.repeatmasker.org/RMBlast.html' -description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary - difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' - for use with RepeatMasker and RepeatModeler.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/'] -sources = ['ncbi-blast-2.10.0+-src.tar.gz'] -patches = [ - ('http://www.repeatmasker.org/isb-2.10.0+-rmblast.patch.gz', 2) -] -checksums = [ - '3acdd9cec01c4f43e56aeaf89049cb8f8013d60b9c1705eced10166967f1d926', # ncbi-blast-2.10.0+-src.tar.gz - 'f17079292d137e73fa7bafac81e10d0be24ad8cbdd263f4baba8f93f25492bd6', # isb-2.10.0+-rmblast.patch.gz -] - -dependencies = [ - ('zlib', '1.2.11'), - ('bzip2', '1.0.6'), - ('Boost', '1.67.0'), -] - -configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt --without-krb5' -configopts += ' --without-openssl --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2' - -sanity_check_paths = { - 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], - 'dirs': ['lib', 'bin'] -} - -moduleclass = 'bio' From 1c22ffce0a209b911804c0a42aefed203c8c9058 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Apr 2020 11:13:07 +0000 Subject: [PATCH 044/431] PLINK version 2.00a2.3LM --- .../p/PLINK/PLINK-2.00a2.3LM-x86_64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb new file mode 100644 index 00000000000..3c2fcedf302 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb @@ -0,0 +1,24 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '2.00a2.3LM-x86_64' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = 'Whole-genome association analysis toolset' + +toolchain = SYSTEM + +source_urls = ['https://s3.amazonaws.com/plink2-assets/alpha2'] +sources = ['plink2_linux_x86_64.zip'] +checksums = ['3fa20a2058df542e928b11d715cc314c01d7c5961525b55fd17a088e6caa9cc9'] + +sanity_check_paths = { + 'files': ['plink2'], + 'dirs': [], +} + +moduleclass = 'bio' From e609bf2874e282ce1b18711ab7b615ed13a4a326 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 7 Apr 2020 16:30:04 +1000 Subject: [PATCH 045/431] Create zsh-5.8-foss-2019b.eb Upgrading zsh version and to a new version of foss toolchain. --- .../easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb new file mode 100644 index 00000000000..39fd603ada6 --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'zsh' +version = '5.8' + +homepage = 'http://www.zsh.org/' +description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [ + ('ncurses', '6.1'), +] + +moduleclass = 'tools' From 09b117dd98b2f696884f5840b70f68912c278d05 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Apr 2020 23:14:57 +0200 Subject: [PATCH 046/431] adding easyconfigs: dftd3-lib-0.9-GCC-8.3.0.eb, DFTB+-19.1-foss-2019b-Python-2.7.16.eb, DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb and patches: dftd3-lib-0.9_fix-extras-syntax.patch --- ...DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb | 90 +++++++++++++++++++ .../DFTB+-19.1-foss-2019b-Python-2.7.16.eb | 76 ++++++++++++++++ .../d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb | 38 ++++++++ .../dftd3-lib-0.9_fix-extras-syntax.patch | 22 +++++ 4 files changed, 226 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb create mode 100644 easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9_fix-extras-syntax.patch diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb new file mode 100644 index 00000000000..c41028e0598 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb @@ -0,0 +1,90 @@ +easyblock = 'ConfigureMake' + +name = 'DFTB+' +version = '19.1' +versionsuffix = '-Python-%(pyver)s-mpi' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True} + +local_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +local_external_extract = 'mkdir -p %s && tar -C %s' % (local_external_dir, local_external_dir) +local_external_extract += ' --strip-components=1 -xzf %%s' + +sources = [ + { + # DFTB+ source code + 'source_urls': ['https://github.com/dftbplus/dftbplus/archive'], + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + # mpifx source code + 'source_urls': ['https://github.com/dftbplus/mpifx/archive'], + 'download_filename': 'dftbplus-%(version)s.tar.gz', + 'filename': 'mpifx-%(version)s.tar.gz', + 'extract_cmd': local_external_extract % ('mpifx', 'mpifx'), + }, + { + # scalapackfx source code + 'source_urls': ['https://github.com/dftbplus/scalapackfx/archive'], + 'download_filename': 'dftbplus-%(version)s.tar.gz', + 'filename': 'scalapackfx-%(version)s.tar.gz', + 'extract_cmd': local_external_extract % ('scalapackfx', 'scalapackfx'), + }, + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': 'd0ea16df2b56d14c7c3dc9329a8d3bac9fea50a0.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': local_external_extract % ('slakos', 'slakos'), + }, +] +checksums = [ + '4d07f5c6102f06999d8cfdb1d17f5b59f9f2b804697f14b3bc562e3ea094b8a8', # DFTB+-19.1.tar.gz + '06f1809da36571d90d0d86dd9e1a697c8a43572a732127b55a400fb5780ef296', # mpifx-19.1.tar.gz + '858ac0e84aa32f227e7e7240d0f62f4cb349996d7a9332cf3483fb066b25b90c', # scalapackfx-19.1.tar.gz + '9b64193368a13ae7c238399da8be2b3730a0f3273f9bf6c8054b2ff57d748823', # slakos-data-19.1.tar.gz +] + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', '-Python-2.7.16'), + ('dftd3-lib', '0.9'), +] + +skipsteps = ['configure'] + +# Use appropriate makefile and flags for this toolchain +prebuildopts = "cp sys/make.x86_64-linux-gnu make.arch && " +prebuildopts += 'sed -i "s|-O2|$OPTFLAGS|g" make.arch && ' + +# Enable MPI and link to OpenBLAS from EB +buildopts = 'WITH_MPI=1 LIB_LAPACK="$LIBLAPACK" ' +# Use DFTD3 from EB +buildopts += 'WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include" ' +buildopts += 'DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3" ' + +runtest = 'test WITH_MPI=1' + +installopts = 'INSTALLDIR="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [('python', '-c "import dptools"')] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..3705472bc21 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,76 @@ +easyblock = 'ConfigureMake' + +name = 'DFTB+' +version = '19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': False} + +local_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +local_external_extract = 'mkdir -p %s && tar -C %s' % (local_external_dir, local_external_dir) +local_external_extract += ' --strip-components=1 -xzf %%s' + +sources = [ + { + # DFTB+ source code + 'source_urls': ['https://github.com/dftbplus/dftbplus/archive'], + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': 'd0ea16df2b56d14c7c3dc9329a8d3bac9fea50a0.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': local_external_extract % ('slakos', 'slakos'), + }, +] +checksums = [ + '4d07f5c6102f06999d8cfdb1d17f5b59f9f2b804697f14b3bc562e3ea094b8a8', # DFTB+-19.1.tar.gz + '9b64193368a13ae7c238399da8be2b3730a0f3273f9bf6c8054b2ff57d748823', # slakos-data-19.1.tar.gz +] + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', '-Python-2.7.16'), + ('arpack-ng', '3.7.0'), + ('dftd3-lib', '0.9'), +] + +skipsteps = ['configure'] + +# Use appropriate makefile and flags for this toolchain +prebuildopts = "cp sys/make.x86_64-linux-gnu make.arch && " +prebuildopts += 'sed -i "s|-O2|$OPTFLAGS|g" make.arch && ' + +# Link to Arpack and OpenBLAS from EB +buildopts = 'WITH_ARPACK=1 ARPACK_LIBS="-L$EBROOTARPACKMINNG/lib -larpack" ARPACK_NEEDS_LAPACK=1 ' +buildopts += 'LIB_LAPACK="$LIBLAPACK" ' +# Use DFTD3 from EB +buildopts += 'WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include" ' +buildopts += 'DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3" ' + +runtest = 'test' + +installopts = 'INSTALLDIR="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [('python', '-c "import dptools"')] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb new file mode 100644 index 00000000000..676567a0aa8 --- /dev/null +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'dftd3-lib' +version = '0.9' + +homepage = 'https://github.com/dftbplus/dftd3-lib' +description = """This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. +The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been +converted to free format and encapsulated into modules.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +github_account = 'dftbplus' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['dftd3-lib-%(version)s_fix-extras-syntax.patch'] +checksums = [ + '0a015659b5179dff1728a109c3e9b095e6bccc5704de9239aa3844008a9a82df', # 0.9.tar.gz + '717e719170258544555bfc33390a70c2573d971c6548d8f2c951a5606ec77f74', # dftd3-lib-0.9_fix-extras-syntax.patch +] + +parallel = 1 + +buildopts = 'FC="$FC" FCFLAGS="$FCFLAGS" LNFLAGS="$LDFLAGS"' + +files_to_copy = [ + (['prg/dftd3', 'test/testapi'], 'bin'), + (['lib/libdftd3.a'], 'lib'), + (['lib/*.mod', 'prg/*.mod'], 'include'), + (['doc/man.pdf', 'CHANGELOG.rst', 'LICENSE', 'README.rst'], 'share'), +] + +sanity_check_paths = { + 'files': ['bin/dftd3', 'bin/testapi', 'lib/libdftd3.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9_fix-extras-syntax.patch b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9_fix-extras-syntax.patch new file mode 100644 index 00000000000..cc64d8b4e23 --- /dev/null +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9_fix-extras-syntax.patch @@ -0,0 +1,22 @@ +Fix syntax of extras.f90 +Author: Alex Domingo (Vrije Universiteit Brussel) +--- prg/extras.f90.orig 2020-04-07 15:53:37.579346000 +0200 ++++ prg/extras.f90 2020-04-07 15:53:47.270025090 +0200 +@@ -285,7 +285,7 @@ + close(11) + + write(*,*) 'checksum (Edisp) ',check +- if (abs(check-etot).gt.1.d-3)stop'something is weired in adisp' ++ if (abs(check-etot).gt.1.d-3) stop 'something is weired in adisp' + + inquire(file='fragment',exist=ex) + if (.not.ex) return +@@ -1746,7 +1746,7 @@ + close(11) + + write(*,*) 'checksum (Edisp) ',check +- if (abs(check-etot).gt.1.d-3)stop'something is weired in adisp' ++ if (abs(check-etot).gt.1.d-3) stop 'something is weired in adisp' + + deallocate(dist,li) + return From 1eab42412fd5c60f5a4bdb3ca0cef0aebd0cb370 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 8 Apr 2020 12:52:50 +0200 Subject: [PATCH 047/431] Alpha: use install_in_subdir instead of final_dir --- .../a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb index eb6939a4552..9c7d3b8eac6 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -41,7 +41,7 @@ components = [ 'sources': [{'download_filename': '%s.zip' % local_pyinc_commit, 'filename': '%(name)s-%(version)s.zip'}], 'checksums': ['9dc9b2bafbfe7a694ff4025164dc6e356989ee89b914691457fb0a474fe66c9e'], 'start_dir': 'thekswenson-%%(name)s-%s' % local_pyinc_commit, - 'final_dir': '%(name)s', + 'install_in_subdir': True, }), (name, version, { 'easyblock': 'Tarball', @@ -53,16 +53,16 @@ components = [ '342d5d37bcfc19a2487c3b08860adc4246736919948b1968f899b0c595d7125d', # Alpha-20190607_fix-email.patch ], 'start_dir': 'thekswenson-%%(namelower)s-%s' % local_alpha_commit, - 'final_dir': '%(namelower)s', + 'install_in_subdir': True, 'keepsymlinks': True, }), ] -local_arch = {'Darwin': 'OSX', 'Linux': 'x86_64'}[OS_TYPE] +local_os = {'Darwin': 'OSX', 'Linux': 'x86_64'}[OS_TYPE] postinstallcmds = [ 'ln -s ${EBROOTGENOMETOOLS} %(installdir)s/%(namelower)s/lib/gtdir', # Alpha provides eqclasses.so for both Linux and OS X - 'cd %%(installdir)s/%%(namelower)s/lib/ccode && ln -s bin_%s/eqclasses.so eqclasses.so' % local_arch, + 'cd %%(installdir)s/%%(namelower)s/lib/ccode && ln -s bin_%s/eqclasses.so eqclasses.so' % local_os, ] sanity_check_paths = { From 4703b68a882e1e8127ed990b65c5045e7f6f0643 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 8 Apr 2020 23:04:06 +0200 Subject: [PATCH 048/431] R v3.6.2: add mRMRe and dHSIC and sync easyconfig in fosscuda --- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 12 ++++++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 62f2f430e2c..97476f4f875 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -2321,6 +2321,12 @@ exts_list = [ ('VSURF', '1.1.0', { 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 6da4bb2e18c..f9b33c5ce1d 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -2316,6 +2316,18 @@ exts_list = [ ('rstan', '2.19.2', { 'checksums': ['31e4ceb9c327cd62873225097ffa538c2ac4cb0547c52271e52e4c7652d508da'], }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), # Specific packages for GPUs ('OpenCL', '0.1-3.1', { 'checksums': ['daff23d777a27cd9d2e67ca8f5db1d29940cf0422708c1ea7e2d9661e3d6ae6f'], From 1cb2dcb559c697a6ede005371389a3e1c052ddc8 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 9 Apr 2020 12:59:54 +0000 Subject: [PATCH 049/431] New EB build file King-2.2.4 --- easybuild/easyconfigs/k/king/king-2.2.4.eb | 29 ++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/k/king/king-2.2.4.eb diff --git a/easybuild/easyconfigs/k/king/king-2.2.4.eb b/easybuild/easyconfigs/k/king/king-2.2.4.eb new file mode 100644 index 00000000000..fb603e4ee6f --- /dev/null +++ b/easybuild/easyconfigs/k/king/king-2.2.4.eb @@ -0,0 +1,29 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'BinariesTarball' + +name = 'king' +version = '2.2.4' +local_version_shorthand = '224' + +homepage = 'https://people.virginia.edu/~wc9c/KING/' +description = """KING is a toolset that makes use of high-throughput +SNP data typically seen in a genome-wide association study (GWAS) or +a sequencing project. Applications of KING include family relationship +inference and pedigree error checking, quality control, population +substructure identification, forensics, gene mapping, etc.""" + +toolchain = {'name': 'system', 'version': ''} + +source_urls = ['https://people.virginia.edu/~wc9c/KING/executables'] +sources = ['Linux-%%(name)s%s.tar.gz' %(local_version_shorthand,)] +checksums = ['405e603875d04e19559598f2b27e5e8113d5b4424388a92fa0b40251897c592b'] + +# files_to_copy = [(['king'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/king'], + 'dirs': [], +} From e1a01b605fdb7292f636a959e745f59bd96c9580 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 9 Apr 2020 14:04:50 +0000 Subject: [PATCH 050/431] Formating corrected --- easybuild/easyconfigs/k/king/king-2.2.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/king/king-2.2.4.eb b/easybuild/easyconfigs/k/king/king-2.2.4.eb index fb603e4ee6f..530d58cabd2 100644 --- a/easybuild/easyconfigs/k/king/king-2.2.4.eb +++ b/easybuild/easyconfigs/k/king/king-2.2.4.eb @@ -18,7 +18,7 @@ substructure identification, forensics, gene mapping, etc.""" toolchain = {'name': 'system', 'version': ''} source_urls = ['https://people.virginia.edu/~wc9c/KING/executables'] -sources = ['Linux-%%(name)s%s.tar.gz' %(local_version_shorthand,)] +sources = ['Linux-%%(name)s%s.tar.gz' % (local_version_shorthand,)] checksums = ['405e603875d04e19559598f2b27e5e8113d5b4424388a92fa0b40251897c592b'] # files_to_copy = [(['king'], 'bin')] From bf080401b30d8d11262ac7b96e6834686631cb46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Apr 2020 20:03:12 +0200 Subject: [PATCH 051/431] adding easyconfigs: AutoMap-1.0-foss-2019b-20200324.eb --- .../AutoMap-1.0-foss-2019b-20200324.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb diff --git a/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb new file mode 100644 index 00000000000..0acf9d32ad4 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'AutoMap' +local_commit = 'ea813dd' +version = '1.0' +versionsuffix = '-20200324' + +homepage = 'https://github.com/mquinodo/AutoMap' +description = "Tool to find regions of homozygosity (ROHs) from sequencing data." + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/mquinodo/AutoMap/archive/'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['cbf60a89984ee0e0119e362be5b620c1f28182d765280bd08c0ba6f9c7697625'] + +dependencies = [ + ('BCFtools', '1.10.2'), + ('BEDTools', '2.29.2'), + ('Perl', '5.30.0'), + ('R', '3.6.2'), +] + +fix_perl_shebang_for = ['Scripts/*.pl'] + +postinstallcmds = ["chmod a+x %(installdir)s/AutoMap_v%(version)s.sh"] + +sanity_check_paths = { + 'files': ['AutoMap_v%(version)s.sh'], + 'dirs': ['Resources', 'Scripts'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 82b3e0de17c7c8a840f85955493c09db0d49b0a5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 10 Apr 2020 18:34:01 +0200 Subject: [PATCH 052/431] add fPIC to build of dftd3-lib v0.9 --- easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb index 676567a0aa8..a0761310c46 100644 --- a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-GCC-8.3.0.eb @@ -9,6 +9,7 @@ The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.""" toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'pic': True} github_account = 'dftbplus' source_urls = [GITHUB_SOURCE] From 2cb2b35c7e9f78834c24ba1012ac1c8c2607b311 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 11 Apr 2020 00:27:15 +0200 Subject: [PATCH 053/431] DFTB+-19.1: use commmon options in build and test steps --- .../DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb | 12 +++++++----- .../d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb | 14 ++++++++------ 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb index c41028e0598..c5575d6c7fd 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16-mpi.eb @@ -65,15 +65,17 @@ skipsteps = ['configure'] # Use appropriate makefile and flags for this toolchain prebuildopts = "cp sys/make.x86_64-linux-gnu make.arch && " -prebuildopts += 'sed -i "s|-O2|$OPTFLAGS|g" make.arch && ' +prebuildopts += 'sed -i "s/-O2/$OPTFLAGS/g" make.arch && ' # Enable MPI and link to OpenBLAS from EB -buildopts = 'WITH_MPI=1 LIB_LAPACK="$LIBLAPACK" ' +local_makeopts = ' WITH_MPI=1 LIB_LAPACK="$LIBLAPACK"' # Use DFTD3 from EB -buildopts += 'WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include" ' -buildopts += 'DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3" ' +local_makeopts += ' WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include"' +local_makeopts += ' DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3"' -runtest = 'test WITH_MPI=1' +buildopts = local_makeopts + +runtest = 'test' + local_makeopts installopts = 'INSTALLDIR="%(installdir)s"' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb index 3705472bc21..145b5a68d44 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-19.1-foss-2019b-Python-2.7.16.eb @@ -50,16 +50,18 @@ skipsteps = ['configure'] # Use appropriate makefile and flags for this toolchain prebuildopts = "cp sys/make.x86_64-linux-gnu make.arch && " -prebuildopts += 'sed -i "s|-O2|$OPTFLAGS|g" make.arch && ' +prebuildopts += 'sed -i "s/-O2/$OPTFLAGS/g" make.arch && ' # Link to Arpack and OpenBLAS from EB -buildopts = 'WITH_ARPACK=1 ARPACK_LIBS="-L$EBROOTARPACKMINNG/lib -larpack" ARPACK_NEEDS_LAPACK=1 ' -buildopts += 'LIB_LAPACK="$LIBLAPACK" ' +local_makeopts = ' WITH_ARPACK=1 ARPACK_LIBS="-L$EBROOTARPACKMINNG/lib -larpack" ARPACK_NEEDS_LAPACK=1' +local_makeopts += ' LIB_LAPACK="$LIBLAPACK"' # Use DFTD3 from EB -buildopts += 'WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include" ' -buildopts += 'DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3" ' +local_makeopts += ' WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include"' +local_makeopts += ' DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3"' -runtest = 'test' +buildopts = local_makeopts + +runtest = 'test' + local_makeopts installopts = 'INSTALLDIR="%(installdir)s"' From 769dafecf62db13591bd385ddca49bc39d4a1c51 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 11 Apr 2020 13:09:25 +0000 Subject: [PATCH 054/431] adding easyconfigs: gradunwarp-1.2.0-foss-2019a-HCP-Python-2.7.15.eb, gradunwarp-1.2.0-foss-2019a-HCP-Python-3.7.2.eb --- ...warp-1.2.0-foss-2019a-HCP-Python-2.7.15.eb | 32 +++++++++++++++++++ ...nwarp-1.2.0-foss-2019a-HCP-Python-3.7.2.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-2.7.15.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-2.7.15.eb new file mode 100644 index 00000000000..02aa3cfa51b --- /dev/null +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-2.7.15.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = "gradunwarp" +version = "1.2.0" +versionsuffix = "-HCP-Python-%(pyver)s" + +homepage = "https://github.com/Washington-University/gradunwarp" +description = """Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3d3c24a821bfbf795301e52d94180fb00461c847f214bf4ae18dd7aea29375a'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +dependencies = [ + ('Python', '2.7.15'), + ('SciPy-bundle', '2019.03'), + ('NiBabel', '2.4.0'), + ('FSL', '6.0.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-3.7.2.eb b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-3.7.2.eb new file mode 100644 index 00000000000..81342648712 --- /dev/null +++ b/easybuild/easyconfigs/g/gradunwarp/gradunwarp-1.2.0-foss-2019a-HCP-Python-3.7.2.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = "gradunwarp" +version = "1.2.0" +versionsuffix = "-HCP-Python-%(pyver)s" + +homepage = "https://github.com/Washington-University/gradunwarp" +description = """Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/Washington-University/gradunwarp/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3d3c24a821bfbf795301e52d94180fb00461c847f214bf4ae18dd7aea29375a'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('NiBabel', '2.4.0'), + ('FSL', '6.0.2', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 0be43bbc98906731bcb0d1671cc500c72936123c Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sun, 12 Apr 2020 17:44:58 +1000 Subject: [PATCH 055/431] Update easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb index 39fd603ada6..27373f17b7c 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb @@ -6,7 +6,7 @@ version = '5.8' homepage = 'http://www.zsh.org/' description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." -toolchain = {'name': 'foss', 'version': '2019b'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] From 31e888f99792aa08e6be50ac7ede1f7fdd711d75 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Apr 2020 10:34:43 +0100 Subject: [PATCH 056/431] adding easyconfigs: SHAP-0.35.0-foss-2019b-Python-3.7.4.eb --- .../SHAP-0.35.0-foss-2019b-Python-3.7.4.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..8705f5f7835 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.35.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,32 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'SHAP' +version = '0.35.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/slundberg/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('scikit-learn', '0.21.3', versionsuffix), + ('tqdm', '4.41.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b9a2a3636918b9cdce4d3c599786b38353fbdca49147b5407a75aee398b1018'] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'data' From 77af3119685b70a70d44f4c24e0f470280e7995e Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 12 Apr 2020 20:25:29 +0000 Subject: [PATCH 057/431] {devel}[GCCcore/8.3.0] GObject-Introspection 1.63.1 w/ Python 3.7.4 missing build dep. pkg-config. --- .../GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb index 868655ead95..7935cf54c15 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,6 +19,7 @@ checksums = ['476379bde8d080d92dd1bb1684f6aa8d79d90ddb81fc85dfa3576e36f9777ab6'] builddependencies = [ ('binutils', '2.32'), + ('pkg-config', '0.29.2'), ('Meson', '0.51.2', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('flex', '2.6.4'), From 99e2bda1f514bd8a4295700348d61f3029ad4acf Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Mon, 13 Apr 2020 07:43:08 +1000 Subject: [PATCH 058/431] Update zsh-5.8-foss-2019b.eb Added checksum --- easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb index 27373f17b7c..20c16b11b9c 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCC', 'version': '8.3.0'} sources = [SOURCELOWER_TAR_XZ] source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +checksums = ['dcc4b54cc5565670a65581760261c163d720991f0d06486da61f8d839b52de27'] dependencies = [ ('ncurses', '6.1'), From 47a42f83218689bc5c3d74d869b6375a9ccc1783 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 10:29:03 +0200 Subject: [PATCH 059/431] fix Perl shebang for RepeatMasker --- .../r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb index 4e2bf2400f3..bb5f15e74c3 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb @@ -29,4 +29,6 @@ dependencies = [ ('HMMER', '3.2.1'), ] +fix_perl_shebang_for = ['RepeatMasker'] + moduleclass = 'bio' From 828de3907221197e0d357944c72e72d8f9ad0a58 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 13 Apr 2020 10:44:28 +0000 Subject: [PATCH 060/431] adding easyconfigs: torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb --- ...ision-0.5.0-fosscuda-2019b-Python-3.7.4.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..c7150d6d3ab --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'torchvision' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eb9afc93df3d174d975ee0914057a9522f5272310b4d56c150b955c287a4d74d'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Python', '3.7.4'), + ('Pillow-SIMD', '6.0.x.post0'), + ('PyTorch', '1.4.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/torchvision'], +} + +moduleclass = 'vis' From 058b2883576b89c9f5e085916a49b2e830f54095 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 13 Apr 2020 14:14:02 +0000 Subject: [PATCH 061/431] adding easyconfigs: GDCM-3.0.5-GCCcore-8.3.0.eb --- .../g/GDCM/GDCM-3.0.5-GCCcore-8.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.5-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.5-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..d8c5896baff --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.5-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.5' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e792144856be3b51661040dabd42d8a66e8cc9300b5d0d7e210131b90d3a399'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), +] + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' From 7838d221de29737a85da8993fa0c639961d931af Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 13 Apr 2020 15:42:35 +0000 Subject: [PATCH 062/431] adding easyconfigs: gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb --- ...ustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..b7dc02069c4 --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '0.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/wookayin/gpustat' +description = 'dstat-like utilization monitor for NVIDIA GPUs' + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('psutil', '5.7.0', { + 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + }), + ('blessings', '1.7', { + 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], + }), + ('nvidia-ml-py3', '7.352.0', { + 'checksums': ['390f02919ee9d73fe63a98c73101061a6b37fa694a793abf56673320f1f51277'], + 'modulename': 'pynvml', + }), + (name, version, { + 'checksums': ['f69135080b2668b662822633312c2180002c10111597af9631bb02e042755b6c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 302d31bdcb4cbb0ecd70aafc19baf8ebec2231be Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 13 Apr 2020 16:00:52 +0000 Subject: [PATCH 063/431] Add download_dep_fail and sanity_pip_check --- .../g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb index b7dc02069c4..8d22e064fd6 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -14,6 +14,8 @@ dependencies = [ ] use_pip = True +download_dep_fail = True +sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From c09d28f25a284501e8c5b157a444523a3f595835 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 13 Apr 2020 16:15:17 +0000 Subject: [PATCH 064/431] Minus download_dep_fail --- .../g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb index 8d22e064fd6..9291ce32844 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -14,7 +14,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From c3baf59a13ca4ec7626439a64f5a8e766ca9eea4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Apr 2020 11:16:37 +0200 Subject: [PATCH 065/431] Check sdist with different python versions --- .github/workflows/unit_tests.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 9e24a544987..12891fa4a77 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -149,6 +149,8 @@ jobs: - name: set up Python uses: actions/setup-python@v1 + with: + python-version: ${{matrix.python}} - name: Create source distribution run: python setup.py sdist From 42e05826b72720fa09daef90eab4fb2ab326b40b Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 14 Apr 2020 12:44:54 +0200 Subject: [PATCH 066/431] adding easyconfigs: Ray-0.8.4-foss-2019b-Python-3.7.4.eb --- .../Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb | 130 ++++++++++++++++++ 1 file changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..1b10c98cb08 --- /dev/null +++ b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,130 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray' +version = '0.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2019b'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('Python', '3.7.4'), + ('Bazel', '0.29.1'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('aiohttp', '3.6.2', { + 'checksums': ['259ab809ff0727d0e834ac5e8a283dc5e3e0ecc30c4d80b3cd17a4139ce1f326'], + }), + ('async-timeout', '3.0.1', { + 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], + }), + ('idna-ssl', '1.1.0', { + 'checksums': ['a933e3bb13da54383f9e8f35dc4f9cb9eb9b3b78c6b36f311254d6d0d92c6c7c'], + }), + ('multidict', '4.7.5', { + 'checksums': ['aee283c49601fa4c13adc64c09c978838a7e812f85377ae130a24d7198c0331e'], + }), + ('typing-extensions', '3.7.4.2', { + 'modulename': 'typing_extensions', + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['79ee589a3caca649a9bfd2a8de4709837400dfa00b6cc81962a1e6a1815969ae'], + }), + ('yarl', '1.4.2', { + 'checksums': ['58cd9c469eced558cd81aa3f484b2924e8897049e06889e8ff2510435b7ef74b'], + }), + ('multidict', '4.7.5', { + 'checksums': ['aee283c49601fa4c13adc64c09c978838a7e812f85377ae130a24d7198c0331e'], + }), + ('click', '7.1.1', { + 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('google', '2.0.3', { + 'checksums': ['ff7d997dbf33be666ed5deb8c5abf5d103c27ec199559b6d994923469e26bb48'], + }), + ('beautifulsoup4', '4.9.0', { + 'modulename': 'bs4', + 'checksums': ['594ca51a10d2b3443cbac41214e12dbb2a1cd57e1a7344659849e2e20ba6a8d8'], + }), + ('soupsieve', '2.0', { + 'checksums': ['e914534802d7ffd233242b785229d5ba0766a7f487385e3f714446a07bf540ae'], + }), + ('grpcio', '1.28.1', { + 'modulename': 'grpc', + 'checksums': ['cbc322c5d5615e67c2a15be631f64e6c2bab8c12505bc7c150948abdaa0bdbac'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('importlib-metadata', '1.6.0', { + 'modulename': 'importlib_metadata', + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + }), + ('pyrsistent', '0.16.0', { + 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('protobuf', '3.11.3', { + 'modulename': 'google.protobuf', + 'checksums': ['c77c974d1dadf246d789f6dad1c24426137c9091e930dbf50e0a29c1fcf00b1f'], + }), + ('py-spy', '0.3.3', { + 'modulename': False, + 'source_tmpl': 'py_spy-%(version)s-py2.py3-none-manylinux1_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['e9d6946741c267fe82aef18d2fc1e095a90a83fb5f3d9fc89b0f20a39613a639'], + }), + ('PyYAML', '5.3.1', { + 'modulename': 'yaml', + 'checksums': ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'], + }), + ('redis', '3.4.1', { + 'checksums': ['0dcfb335921b88a850d461dc255ff4708294943322bd55de6cfd68972490ca1f'], + }), + # (name, version, { + # 'source_tmpl': '%(namelower)s-%(version)s-cp37-cp37m-manylinux1_x86_64.whl', + # 'unpack_sources': False, + # 'checksums': ['f2cca186a9f8a18f9d58eadcd8ea126addc3192e922f36a7ced46b8b8904ac65'], + # }), + (name, version, { + 'source_urls': ['https://github.com/ray-project/ray/archive/'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_editable': True, + 'unpack_sources': True, + # 'checksums': ['f2cca186a9f8a18f9d58eadcd8ea126addc3192e922f36a7ced46b8b8904ac65'], + }), + +] + +local_bin_files = ['google', 'jsonschema', 'py-spy', 'ray', 'rllib', 'tune'] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'ray --help' +] + +moduleclass = 'bio' From 27ea7ea5cee3afa05125140c2418f8de1c2fdafe Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 14 Apr 2020 12:46:09 +0200 Subject: [PATCH 067/431] removed comments --- .../r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb index 1b10c98cb08..f1be3a65860 100644 --- a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb @@ -103,17 +103,10 @@ exts_list = [ ('redis', '3.4.1', { 'checksums': ['0dcfb335921b88a850d461dc255ff4708294943322bd55de6cfd68972490ca1f'], }), - # (name, version, { - # 'source_tmpl': '%(namelower)s-%(version)s-cp37-cp37m-manylinux1_x86_64.whl', - # 'unpack_sources': False, - # 'checksums': ['f2cca186a9f8a18f9d58eadcd8ea126addc3192e922f36a7ced46b8b8904ac65'], - # }), (name, version, { - 'source_urls': ['https://github.com/ray-project/ray/archive/'], - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'use_pip_editable': True, - 'unpack_sources': True, - # 'checksums': ['f2cca186a9f8a18f9d58eadcd8ea126addc3192e922f36a7ced46b8b8904ac65'], + 'source_tmpl': '%(namelower)s-%(version)s-cp37-cp37m-manylinux1_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['f2cca186a9f8a18f9d58eadcd8ea126addc3192e922f36a7ced46b8b8904ac65'], }), ] From b3ed78e8a6b7a692f7e7b3e89b3a86d4bd266b62 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 4 Feb 2020 15:24:41 +0100 Subject: [PATCH 068/431] adding easyconfigs: rstudio-1.2.5033-fosscuda-2019b-Java-11.eb and patches: rstudio-1.2.5033_fix_boost_170_compat.patch, rstudio-1.2.5033_update_gwt.patch --- ...rstudio-1.2.5033-fosscuda-2019b-Java-11.eb | 54 +++++++++ ...studio-1.2.5033_fix_boost_170_compat.patch | 105 ++++++++++++++++++ .../rstudio/rstudio-1.2.5033_update_gwt.patch | 22 ++++ 3 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb create mode 100644 easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_fix_boost_170_compat.patch create mode 100644 easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb new file mode 100644 index 00000000000..bd47231dbb2 --- /dev/null +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMake' + +name = 'rstudio' +version = '1.2.5033' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.rstudio.com/' +description = """This RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'rstudio-1.2.5033_fix_boost_170_compat.patch', + 'rstudio-1.2.5033_update_gwt.patch', +] +checksums = [ + 'ff5115bda56ee0fdee0ae2eb014ce5379774aeb3714a257a52da5b91a95e4408', # v1.2.5033.tar.gz + 'd252111e28a7de8602b4df1f66b36dded260061f094b504895e5c789f8681091', # rstudio-1.2.5033_fix_boost_170_compat.patch + 'b09e9905aab81cbeb18263726c2623d9a405f70560dbb1d9cae5b8ea1f557539', # rstudio-1.2.5033_update_gwt.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('CMake', '3.15.3'), + ('ant', '1.10.7', '-Java-%(javaver)s', True), +] + +dependencies = [ + ('Boost', '1.71.0'), + ('R', '3.6.2'), + ('Java', '11', '', True), +] + +osdependencies = ['pam-devel'] + +build_type = "Release" +local_dep_dir = "%(builddir)s/%(name)s-%(version)s/dependencies/common" +preconfigopts = ("(cd %s && ./install-dictionaries && " + "./install-pandoc && ./install-mathjax && ./install-gwt) && ") % local_dep_dir +configopts = "-DRSTUDIO_TARGET=Server -DRSTUDIO_BOOST_SIGNALS_VERSION=2" + +sanity_check_paths = { + 'files': ["bin/rstudio-server"], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_fix_boost_170_compat.patch b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_fix_boost_170_compat.patch new file mode 100644 index 00000000000..9afec1c8d30 --- /dev/null +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_fix_boost_170_compat.patch @@ -0,0 +1,105 @@ +From 33c2c42d40ad97d97ca3907df51059cd2ce76fe3 Mon Sep 17 00:00:00 2001 +From: Kevin Ushey +Date: Tue, 3 Sep 2019 13:23:23 -0700 +Subject: [PATCH] first pass at Boost 1.70 support + +--- + src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp | 6 ++++-- + src/cpp/ext/websocketpp/transport/asio/connection.hpp | 2 +- + src/cpp/ext/websocketpp/transport/asio/endpoint.hpp | 10 +++------- + .../ext/websocketpp/transport/asio/security/none.hpp | 3 +-- + 4 files changed, 9 insertions(+), 12 deletions(-) + +diff --git a/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp b/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp +index 14e4114e15..334afb9790 100644 +--- a/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp ++++ b/src/cpp/core/include/core/http/TcpIpAsyncConnector.hpp +@@ -55,7 +55,8 @@ class TcpIpAsyncConnector : + public: + TcpIpAsyncConnector(boost::asio::io_service& ioService, + boost::asio::ip::tcp::socket* pSocket) +- : pSocket_(pSocket), ++ : service_(ioService), ++ pSocket_(pSocket), + resolver_(ioService), + isConnected_(false), + hasFailed_(false) +@@ -78,7 +79,7 @@ class TcpIpAsyncConnector : + { + // start a timer that will cancel any outstanding asynchronous operations + // when it elapses if the connection operation has not succeeded +- pConnectionTimer_.reset(new boost::asio::deadline_timer(resolver_.get_io_service(), timeout)); ++ pConnectionTimer_.reset(new boost::asio::deadline_timer(service_, timeout)); + pConnectionTimer_->async_wait(boost::bind(&TcpIpAsyncConnector::onConnectionTimeout, + TcpIpAsyncConnector::shared_from_this(), + boost::asio::placeholders::error)); +@@ -233,6 +234,7 @@ class TcpIpAsyncConnector : + } + + private: ++ boost::asio::io_service& service_; + boost::asio::ip::tcp::socket* pSocket_; + boost::asio::ip::tcp::resolver resolver_; + ConnectedHandler connectedHandler_; +diff --git a/src/cpp/ext/websocketpp/transport/asio/connection.hpp b/src/cpp/ext/websocketpp/transport/asio/connection.hpp +index 395632c3f3..ef35d295ac 100644 +--- a/src/cpp/ext/websocketpp/transport/asio/connection.hpp ++++ b/src/cpp/ext/websocketpp/transport/asio/connection.hpp +@@ -296,7 +296,7 @@ class connection : public config::socket_type::socket_con_type { + */ + timer_ptr set_timer(long duration, timer_handler callback) { + timer_ptr new_timer = lib::make_shared( +- lib::ref(*m_io_service), ++ *m_io_service, + boost::posix_time::milliseconds(duration) + ); + +diff --git a/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp b/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp +index ef3b07db46..b418060a85 100644 +--- a/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp ++++ b/src/cpp/ext/websocketpp/transport/asio/endpoint.hpp +@@ -183,8 +183,7 @@ class endpoint : public config::socket_type { + + m_io_service = ptr; + m_external_io_service = true; +- m_acceptor = lib::make_shared( +- lib::ref(*m_io_service)); ++ m_acceptor = lib::make_shared(*m_io_service); + + m_state = READY; + ec = lib::error_code(); +@@ -609,9 +608,7 @@ class endpoint : public config::socket_type { + * @since 0.3.0 + */ + void start_perpetual() { +- m_work = lib::make_shared( +- lib::ref(*m_io_service) +- ); ++ m_work = lib::make_shared(*m_io_service); + } + + /// Clears the endpoint's perpetual flag, allowing it to exit when empty +@@ -775,8 +772,7 @@ class endpoint : public config::socket_type { + + // Create a resolver + if (!m_resolver) { +- m_resolver = lib::make_shared( +- lib::ref(*m_io_service)); ++ m_resolver = lib::make_shared(*m_io_service); + } + + std::string proxy = tcon->get_proxy(); +diff --git a/src/cpp/ext/websocketpp/transport/asio/security/none.hpp b/src/cpp/ext/websocketpp/transport/asio/security/none.hpp +index 14b6f8b5f7..5876c981ce 100644 +--- a/src/cpp/ext/websocketpp/transport/asio/security/none.hpp ++++ b/src/cpp/ext/websocketpp/transport/asio/security/none.hpp +@@ -166,8 +166,7 @@ class connection : public lib::enable_shared_from_this { + return socket::make_error_code(socket::error::invalid_state); + } + +- m_socket = lib::make_shared( +- lib::ref(*service)); ++ m_socket = lib::make_shared(*service); + + m_state = READY; + diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch new file mode 100644 index 00000000000..bf95816ddaa --- /dev/null +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch @@ -0,0 +1,22 @@ +--- a/dependencies/common/install-gwt 2020-02-04 11:16:49.907923640 +0000 ++++ b/dependencies/common/install-gwt 2020-02-04 11:16:38.932802049 +0000 +@@ -61,7 +61,7 @@ + fi + + # gwt sdk +-GWT_SDK_VER=2.8.1 ++GWT_SDK_VER=2.8.2 + GWT_SDK=gwt-$GWT_SDK_VER + GWT_SDK_ZIP=$GWT_SDK.zip + if [ -d "$LIB_DIR/gwt/$GWT_SDK_VER" ] +--- a/src/gwt/build.xml 2020-02-04 11:24:38.224107923 +0000 ++++ b/src/gwt/build.xml 2020-02-04 11:24:57.542321679 +0000 +@@ -29,7 +29,7 @@ + classpath="${tools.dir}/compiler/compiler.jar"/> + + +- ++ + + + From 06364476f53f237afd71f77501fc11b6d6ed4c63 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Apr 2020 14:14:21 +0200 Subject: [PATCH 069/431] Add patch authorship and description --- .../r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb | 2 +- .../easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb index bd47231dbb2..0f047779aa8 100644 --- a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb @@ -23,7 +23,7 @@ patches = [ checksums = [ 'ff5115bda56ee0fdee0ae2eb014ce5379774aeb3714a257a52da5b91a95e4408', # v1.2.5033.tar.gz 'd252111e28a7de8602b4df1f66b36dded260061f094b504895e5c789f8681091', # rstudio-1.2.5033_fix_boost_170_compat.patch - 'b09e9905aab81cbeb18263726c2623d9a405f70560dbb1d9cae5b8ea1f557539', # rstudio-1.2.5033_update_gwt.patch + 'e0b4e165e45357bfaaefbd6f20a7ee69701c56bd623fa2bdfe6df4a1cabc4415', # rstudio-1.2.5033_update_gwt.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch index bf95816ddaa..29de7cf47e4 100644 --- a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033_update_gwt.patch @@ -1,3 +1,6 @@ +From: edmondac-admin +Date: Tue, 4 Feb 2020 11:45:35 +0000 +Subject: Update bundled GWT to 2.8.2 which compiles with Java > 8 --- a/dependencies/common/install-gwt 2020-02-04 11:16:49.907923640 +0000 +++ b/dependencies/common/install-gwt 2020-02-04 11:16:38.932802049 +0000 @@ -61,7 +61,7 @@ From 339d4037de2b9cf39e772f3434537e2c3e145e05 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Feb 2020 08:49:41 +0100 Subject: [PATCH 070/431] [R 3.6.2] Fix build on Power9 --- .../easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 8 ++++++- .../easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 8 ++++++- .../r/R/R-3.6.2_fix_long_dbl_on_ppc.patch | 24 +++++++++++++++++++ 3 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/R/R-3.6.2_fix_long_dbl_on_ppc.patch diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 62f2f430e2c..416acbb0d19 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -9,7 +9,13 @@ toolchain = {'name': 'foss', 'version': '2019b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954'] +patches = [ + '%(name)s-%(version)s_fix_long_dbl_on_ppc.patch', +] +checksums = [ + 'bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954', # R-3.6.2.tar.gz + '833b80f9a62751eae9cfbad6116542acf932e9c6511235145be32264aacdce69', # R-3.6.2_fix_long_dbl_on_ppc.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 6da4bb2e18c..0beb9e40e53 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -9,7 +9,13 @@ toolchain = {'name': 'fosscuda', 'version': '2019b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954'] +patches = [ + '%(name)s-%(version)s_fix_long_dbl_on_ppc.patch', +] +checksums = [ + 'bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954', # R-3.6.2.tar.gz + '833b80f9a62751eae9cfbad6116542acf932e9c6511235145be32264aacdce69', # R-3.6.2_fix_long_dbl_on_ppc.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-3.6.2_fix_long_dbl_on_ppc.patch b/easybuild/easyconfigs/r/R/R-3.6.2_fix_long_dbl_on_ppc.patch new file mode 100644 index 00000000000..ccc9511bb45 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.6.2_fix_long_dbl_on_ppc.patch @@ -0,0 +1,24 @@ +On powerpc64, gcc is compiled with -mlong-double-128, and the long double +format used on PPC is IBM's 128bit long double which is two doubles added +together. As a result, gcc can't safely do const assignments to long +doubles on ppc64, so it dies there. +Taken from https://r.789695.n4.nabble.com/Build-failure-on-powerpc64-td4760605.html +Index: src/main/arithmetic.c +=================================================================== +--- src/main/arithmetic.c (Revision 77586) ++++ src/main/arithmetic.c (Revision 77587) +@@ -176,8 +176,14 @@ + #endif + } + ++ + #if HAVE_LONG_DOUBLE && (SIZEOF_LONG_DOUBLE > SIZEOF_DOUBLE) ++# ifdef __PPC64__ ++ // PowerPC 64 (when gcc has -mlong-double-128) fails constant folding with LDOUBLE ++# define q_1_eps (1 / LDBL_EPSILON) ++# else + static LDOUBLE q_1_eps = 1 / LDBL_EPSILON; ++# endif + #else + static double q_1_eps = 1 / DBL_EPSILON; + #endif From f22e33f3298cf2939d71502ae7aff98a32373f0b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 10 Feb 2020 12:45:37 +0100 Subject: [PATCH 071/431] [liquidSVM] Fix building on Power9 --- .../easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 8 +++- .../easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 8 +++- .../r/R/liquidSVM-1.2.4-fix_ppc_build.patch | 48 +++++++++++++++++++ 3 files changed, 62 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/R/liquidSVM-1.2.4-fix_ppc_build.patch diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 416acbb0d19..487b1ac3207 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -2105,7 +2105,13 @@ exts_list = [ 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], }), ('liquidSVM', '1.2.4', { - 'checksums': ['15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'], + 'patches': ['liquidSVM-1.2.4-fix_ppc_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', + '21e65c8ff3f14678e43c19b4f8c36fce9bed796965abf161a147040941fc55ab', # liquidSVM-1.2.4-fix_ppc_build.patch + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 0beb9e40e53..e5d195b4cc8 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -2106,7 +2106,13 @@ exts_list = [ 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], }), ('liquidSVM', '1.2.4', { - 'checksums': ['15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'], + 'patches': ['liquidSVM-1.2.4-fix_ppc_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', + '21e65c8ff3f14678e43c19b4f8c36fce9bed796965abf161a147040941fc55ab', # liquidSVM-1.2.4-fix_ppc_build.patch + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], diff --git a/easybuild/easyconfigs/r/R/liquidSVM-1.2.4-fix_ppc_build.patch b/easybuild/easyconfigs/r/R/liquidSVM-1.2.4-fix_ppc_build.patch new file mode 100644 index 00000000000..32d224dd29b --- /dev/null +++ b/easybuild/easyconfigs/r/R/liquidSVM-1.2.4-fix_ppc_build.patch @@ -0,0 +1,48 @@ +The code requires C++11 but nvcc is not passed any flag for it, do that to avoid 'error: identifier "__ieee128" is undefined' on PPC +Use uppercase __PPC64__ to detect PPC 64bit (defined by GCC) +diff -aur liquidSVM-orig/MD5 liquidSVM/MD5 +--- liquidSVM-orig/MD5 2020-02-20 15:51:17.387058566 +0100 ++++ liquidSVM/MD5 2020-02-20 16:48:06.042078399 +0100 +@@ -66,7 +66,7 @@ + e0ea06f050a2ae8ed2f2e401d968f0ce *man/test.liquidSVM.Rd + 8874fc45419e3174bf06013d887f6582 *man/trainSVMs.Rd + 4cf2abf7c6d415a4a8cd7f5dee2df959 *man/write.liquidData.Rd +-854c1eecccd169acdb80b03ad6d768dc *src/Makevars.in ++8c4346267f7b7f649ff27fb5288d4e23 *src/Makevars.in + e6d47b428caa2cc55798b431cb5e504f *src/kernel_calculator.cpp + 13af8529f5c2bccd4ea03288e9adf908 *src/kernel_calculator.h + dc2c86cbe61e7b7c5dd433f9fa41fac6 *src/liquidSVM.cpp +@@ -155,7 +155,7 @@ + 8b39ec05680bf3416bc1de3ad92f043f *src/sources/shared/system_support/cuda_simple_vector_operations.h + 806ca83732bff4b1b89adfc3494e90da *src/sources/shared/system_support/full_64bit_support.h + dfb08cdb449d490d86dd33bee186aac5 *src/sources/shared/system_support/memory_allocation.cpp +-aec0000be577e69e88c040b641d6818a *src/sources/shared/system_support/memory_allocation.h ++8ea6ac178dd02e862eefa36b789b1711 *src/sources/shared/system_support/memory_allocation.h + 683d4ee517b1c760dc410c69c5508ce2 *src/sources/shared/system_support/memory_allocation.ins.cpp + cbd209324ad752e19be10d8975d65e2f *src/sources/shared/system_support/os_specifics.h + 54e8583d2e8e269ff2b6d7a79d57cbd5 *src/sources/shared/system_support/parallel_control.cpp +diff -aur liquidSVM-orig/src/Makevars.in liquidSVM/src/Makevars.in +--- liquidSVM-orig/src/Makevars.in 2020-02-20 15:51:17.377058962 +0100 ++++ liquidSVM/src/Makevars.in 2020-02-20 16:47:44.042949538 +0100 +@@ -39,7 +39,7 @@ + # The architecure flag can be set to higher values, if the hardware supports this. + # The value below should be safe for essentially all non stone-age systems. + +-NVCCFLAGS= -arch sm_30 -L$(CUDA_LIB_PATH) -DCOMPILE_WITH_CUDA__ -U__SSE2__ -U__AVX__ ++NVCCFLAGS= -arch sm_30 -L$(CUDA_LIB_PATH) -DCOMPILE_WITH_CUDA__ -U__SSE2__ -U__AVX__ -std=c++11 + + + #----------- CUDA related flags for GCC ---------------------------------------------------- +diff -aur liquidSVM-orig/src/sources/shared/system_support/memory_allocation.h liquidSVM/src/sources/shared/system_support/memory_allocation.h +--- liquidSVM-orig/src/sources/shared/system_support/memory_allocation.h 2020-02-20 15:51:17.377058962 +0100 ++++ liquidSVM/src/sources/shared/system_support/memory_allocation.h 2020-02-20 15:56:04.905673381 +0100 +@@ -42,7 +42,7 @@ + + // Check for GCC + #if __GNUC__ +- #if __x86_64__ || __ppc64__ ++ #if __x86_64__ || __ppc64__ || __PPC64__ + #define SYSTEM_WITH_64BIT + #else + #define SYSTEM_WITH_32BIT + From 40e1cb25a371ce427a3703eaf40b48f6c9b04db9 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 14 Apr 2020 14:13:36 +0000 Subject: [PATCH 072/431] Change of how to do versioning, download from Github instead of Amazon --- ...K-2.00a2.3LM-x86_64.eb => PLINK-2.00a2.3_x86_64.eb} | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PLINK/{PLINK-2.00a2.3LM-x86_64.eb => PLINK-2.00a2.3_x86_64.eb} (65%) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb similarity index 65% rename from easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb rename to easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb index 3c2fcedf302..c6e7e31da16 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3LM-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb @@ -5,15 +5,19 @@ easyblock = 'PackedBinary' name = 'PLINK' -version = '2.00a2.3LM-x86_64' +version = '2.00a2.3_x86_64' +local_version = '2.00a2.3' homepage = 'https://www.cog-genomics.org/plink/2.0/' description = 'Whole-genome association analysis toolset' toolchain = SYSTEM -source_urls = ['https://s3.amazonaws.com/plink2-assets/alpha2'] -sources = ['plink2_linux_x86_64.zip'] +source_urls = ['https://github.com/chrchang/plink-ng/releases/download/v%s' % (local_version,)] +sources = [{ + 'download_filename': 'plink2_linux_x86_64.zip', + 'filename': 'plink2_linux_%(version)s.zip', +}] checksums = ['3fa20a2058df542e928b11d715cc314c01d7c5961525b55fd17a088e6caa9cc9'] sanity_check_paths = { From 5429d6dfdcf07911faceed6cf761e117aafb90ed Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 14 Apr 2020 14:26:33 +0000 Subject: [PATCH 073/431] Change of how to do versioning, changed tool-chain, minor style corrections --- easybuild/easyconfigs/k/king/king-2.2.4.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/k/king/king-2.2.4.eb b/easybuild/easyconfigs/k/king/king-2.2.4.eb index 530d58cabd2..4f9dd94cc27 100644 --- a/easybuild/easyconfigs/k/king/king-2.2.4.eb +++ b/easybuild/easyconfigs/k/king/king-2.2.4.eb @@ -6,7 +6,6 @@ easyblock = 'BinariesTarball' name = 'king' version = '2.2.4' -local_version_shorthand = '224' homepage = 'https://people.virginia.edu/~wc9c/KING/' description = """KING is a toolset that makes use of high-throughput @@ -15,15 +14,15 @@ a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = SYSTEM source_urls = ['https://people.virginia.edu/~wc9c/KING/executables'] -sources = ['Linux-%%(name)s%s.tar.gz' % (local_version_shorthand,)] +sources = ['Linux-%%(name)s%s.tar.gz' % version.replace('.', '')] checksums = ['405e603875d04e19559598f2b27e5e8113d5b4424388a92fa0b40251897c592b'] -# files_to_copy = [(['king'], 'bin')] - sanity_check_paths = { 'files': ['bin/king'], 'dirs': [], } + +moduleclass = 'bio' From 696874dda6f65232a9225bd3ccecd17abf85c016 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 14 Apr 2020 14:42:41 +0000 Subject: [PATCH 074/431] Change of how to do versioning, thanks lexming --- easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb index c6e7e31da16..5e5f821dbb3 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3_x86_64.eb @@ -6,14 +6,13 @@ easyblock = 'PackedBinary' name = 'PLINK' version = '2.00a2.3_x86_64' -local_version = '2.00a2.3' homepage = 'https://www.cog-genomics.org/plink/2.0/' description = 'Whole-genome association analysis toolset' toolchain = SYSTEM -source_urls = ['https://github.com/chrchang/plink-ng/releases/download/v%s' % (local_version,)] +source_urls = ['https://github.com/chrchang/plink-ng/releases/download/v%s' % version.replace('_x86_64', '')] sources = [{ 'download_filename': 'plink2_linux_x86_64.zip', 'filename': 'plink2_linux_%(version)s.zip', From 8e1f2ad29c0465e05ba8c77cb48e9abe0a1b05ad Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 14 Apr 2020 22:45:04 +0800 Subject: [PATCH 075/431] adding easyconfigs: EasyBuild-4.2.0.eb --- .../e/EasyBuild/EasyBuild-4.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb new file mode 100644 index 00000000000..b48d53735da --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.2.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/79/8d/734c9328be100fa088eea370c8a9419fcd00a1d2ffb8e2d8b48e1ea91ccc/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/3a/2c/44bd425b407229f49d2a4b849c57366ccabcfc6a44524772c11954dbc833/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/c3/5e/9e03725be46b8cad207b5ef5f0e80e2eb205f4e6bd80edb731f48cf5d4a5/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'e260ad9c921c10873b0e3b6b322a42e5732fbed905cb50f5d189a4f54f4ad327', # easybuild-framework-4.2.0.tar.gz + '3619fcd79b8c4f9ff3c913f8d76586c4388f1ec48c90d99140bd230da5631776', # easybuild-easyblocks-4.2.0.tar.gz + '81b57120e0e3ba0d97defafa677a7449fa355b34dfa6ecaca190b5bc94fedffd', # easybuild-easyconfigs-4.2.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From ce736e5e46fbd61afdbbaa241c7277ae3510ac94 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 14 Apr 2020 17:33:43 +0200 Subject: [PATCH 076/431] adding easyconfigs: QuantumESPRESSO-6.5-intel-2019b.eb --- .../QuantumESPRESSO-6.5-intel-2019b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb new file mode 100644 index 00000000000..195349a44c6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.5-intel-2019b.eb @@ -0,0 +1,43 @@ +name = 'QuantumESPRESSO' +version = '6.5' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'wannier90-3.0.0.tar.gz', 'download_filename': 'v3.0.0.tar.gz'}, +] +checksums = [ + 'b4a3a150d67f0f5f86df86c48e3d42f93daaee13a4b2509bb45f45c7fe84c573', # qe-6.5-ReleasePack.tgz + '8c55e893d0222e58952cf456028e884364e946f9a0536fe49ccfbe51bf1a8e9c', # qe-gipaw-6.5.tar.gz + 'f196e441dcd7b67159a1d09d2d7de2893b011a9f03aab6b30c4703ecbf20fe5b', # wannier90-3.0.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('ELPA', '2019.11.001'), + ('libxc', '4.3.4'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From b0f80ea95234aa7f7d56dc4209b72e5d57034452 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 17:56:25 +0200 Subject: [PATCH 077/431] remove PR #10380 from EasyBuild v4.2.0 release notes (was merged into 'develop' branch after forking off '4.2.x' branch) --- RELEASE_NOTES | 1 - 1 file changed, 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 56718b85f44..ffd38901557 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -101,7 +101,6 @@ feature release - ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (#10326) - fix undefined reference error due to libxc 4.3.4 built with CMake (#10356) - fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (#10361) - - add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (#10380) - update checksums and homepage in tbb easyconfigs (#10285) - other changes: - use new custom easyblock in recent CMake easyconfigs (#9871, #9923) From f14b84adf8d0a9c47c0812b107fb2b398962d964 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 17:56:48 +0200 Subject: [PATCH 078/431] bump version to 4.2.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index be548c694ed..f0a4f882e5a 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.2.0' +VERSION = '4.2.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 63c2249f0e8d8af665e12f111657066d478415f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Apr 2020 12:07:29 +0200 Subject: [PATCH 079/431] adding easyconfigs: Multiwfn-3.6-intel-2019b.eb --- .../m/Multiwfn/Multiwfn-3.6-intel-2019b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb diff --git a/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb new file mode 100644 index 00000000000..e1d141ed435 --- /dev/null +++ b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Multiwfn' +version = '3.6' + +homepage = 'http://sobereva.com/multiwfn/' +description = """Multiwfn is an extremely powerful program for realizingi + electronic wavefunction analysis, which is a key ingredient of quantum + chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly + and flexible, it supports almost all of the most important wavefunction + analysis methods.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = [ + 'http://sobereva.com/multiwfn/misc/', + 'http://sobereva.com/multiwfn/old/%(version)s/', +] +sources = ['%(name)s_%(version)s_src_Linux.zip'] +checksums = ['843f2ff0cba8e567b8c537c54ae68a4c242aaf2f08e828331a2d9cbfc7ba0a80'] + +# Make sure the noGUI.sh script runs in bash. +prebuildopts = '/bin/bash noGUI.sh && cd noGUI && ' + +files_to_copy = [(['noGUI/Multiwfn'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Multiwfn'], + 'dirs': [], +} + +moduleclass = 'chem' From 27dd3cb507bf07296433ec90205753ca4319ac0f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Apr 2020 12:23:51 +0200 Subject: [PATCH 080/431] adding easyconfigs: PyMC3-3.8-foss-2019b-Python-3.7.4.eb, netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb --- ...f4-python-1.5.3-foss-2019b-Python-3.7.4.eb | 56 +++++++++++++++++++ .../PyMC3-3.8-foss-2019b-Python-3.7.4.eb | 46 +++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..3be778b6f3e --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.3-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # for numpy + ('netCDF', '4.7.1'), + ('cURL', '7.66.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cftime', '1.1.1.2', { + 'checksums': ['35711b5ec3928b9e724817bfa1b7325da205788ee04eae9166cbcd96ea7976a6'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'checksums': [ + '2a3ca855848f4bbf07fac366da77a681fcead18c0a8813d91d46302f562dc3be', # netCDF4-1.5.3.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..1c2ce140ea7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.8-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,46 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyMC3' +version = '3.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://docs.pymc.io/' +description = """Probabilistic Programming in Python: +Bayesian Modeling and Probabilistic Machine Learning with Theano""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # for numpy + ('Theano', '1.0.4', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('tqdm', '4.41.1'), + ('netcdf4-python', '1.5.3', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('xarray', '0.15.1', { + 'checksums': ['64e3138d87b641e22fe7a003c94abc685896b247b63e434505c1e6b38c91a8fb'], + }), + ('arviz', '0.7.0', { + 'checksums': ['6872abec18e457c62e2f05591d89befd521b6e680fc57ea6560c6dd12da4f62b'], + }), + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('pymc3', version, { + 'checksums': ['1bb2915e4a29877c681ead13932b0b7d276f7f496e9c3f09ba96b977c99caf00'], + }), +] + +moduleclass = 'math' From befd6d5e35600a3b0b2e96756888f9ee1e13451d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Apr 2020 13:51:15 +0200 Subject: [PATCH 081/431] adding easyconfigs: ArviZ-0.7.0-foss-2019b-Python-3.7.4.eb --- .../ArviZ-0.7.0-foss-2019b-Python-3.7.4.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.7.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.7.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.7.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..f281e0b5035 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.7.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'ArviZ' +version = '0.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6872abec18e457c62e2f05591d89befd521b6e680fc57ea6560c6dd12da4f62b'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # numpy, scipy, pandas + ('netcdf4-python', '1.5.3', versionsuffix), + ('xarray', '0.15.1', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From 9b1816f6e8ecb75f6aa809163224606bff622f47 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 15 Apr 2020 16:16:18 +0200 Subject: [PATCH 082/431] Update flex-2.6.4.eb make flex/2.6.4 depend on Bison 3.3.2 to streamline the bootstrap process of a toolchain --- easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index 9fc7b3acbde..76f531338a8 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] builddependencies = [ - ('Bison', '3.0.4'), + ('Bison', '3.3.2'), ('help2man', '1.47.4'), ] From 7d9620c74de0a75d782c54cb41c7db2230dc9fe1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 15 Apr 2020 11:12:24 +0200 Subject: [PATCH 083/431] adding easyconfigs: CubeLib-4.4.4-GCCcore-8.3.0.eb, CubeWriter-4.4.3-GCCcore-8.3.0.eb, OPARI2-2.0.5-GCCcore-8.3.0.eb, OTF2-2.2-GCCcore-8.3.0.eb, PAPI-6.0.0-GCCcore-8.3.0.eb, PDT-3.25-GCCcore-8.3.0.eb, SIONlib-1.7.6-GCCcore-8.3.0-tools.eb, Score-P-6.0-gompic-2019b.eb --- .../c/CubeLib/CubeLib-4.4.4-GCCcore-8.3.0.eb | 56 +++++++++++++++++ .../CubeWriter-4.4.3-GCCcore-8.3.0.eb | 55 ++++++++++++++++ .../o/OPARI2/OPARI2-2.0.5-GCCcore-8.3.0.eb | 45 ++++++++++++++ .../o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb | 49 +++++++++++++++ .../p/PAPI/PAPI-6.0.0-GCCcore-8.3.0.eb | 55 ++++++++++++++++ .../p/PDT/PDT-3.25-GCCcore-8.3.0.eb | 39 ++++++++++++ .../SIONlib-1.7.6-GCCcore-8.3.0-tools.eb | 51 +++++++++++++++ .../s/Score-P/Score-P-6.0-gompic-2019b.eb | 62 +++++++++++++++++++ 8 files changed, 412 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.4-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.5-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-8.3.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..25e3ff6e0dc --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.4-GCCcore-8.3.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.4.4' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + 'adb8216ee3b7701383884417374e7ff946edb30e56640307c65465187dca7512', # cubelib-4.4.4.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..241e8f91ebf --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.3-GCCcore-8.3.0.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.4.3' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = [ + '93fff6cc1e8b0780f0171ef5302a2e1a257f99b6383fbfc1b9b82f925ceff501', # cubew-4.4.3.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.5-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..3efc93b2ab0 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.5-GCCcore-8.3.0.eb @@ -0,0 +1,45 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.5' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://www.vi-hps.org/cms/upload/packages/opari2/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '9034dd7596ac2176401090fd5ced45d0ab9a9404444ff767f093ccce68114ef5', # opari2-2.0.5.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..2e6c29be6c4 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb @@ -0,0 +1,49 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.2' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://www.vi-hps.org/cms/upload/packages/otf2/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + 'd0519af93839dc778eddca2ce1447b1ee23002c41e60beac41ea7fe43117172d', # otf2-2.2.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.32'), + # SIONlib container support (optional): + ('SIONlib', '1.7.6', '-tools'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ['otf2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..20a338a83fa --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0-GCCcore-8.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '6.0.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3442709dae3405c2845b304c06a8b15395ecf4f3899a89ceb4d715103cb4055f'] + +builddependencies = [ + ('binutils', '2.32'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0286d5e26da --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb @@ -0,0 +1,39 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'PDT' +version = '3.25' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = [ + '1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be', # pdtoolkit-3.25.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.32'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-8.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-8.3.0-tools.eb new file mode 100644 index 00000000000..eaac41fd9e1 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-8.3.0-tools.eb @@ -0,0 +1,51 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.6' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] +sources = ['sionlib-%(version)sl.tar.gz'] +checksums = [ + '2c220390ef63d001f8ab02c380087187ea02ad2bfc5956e05ecaa0725a6f9942', # sionlib-1.7.6l.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.32'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb new file mode 100644 index 00000000000..d2df82c6b38 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb @@ -0,0 +1,62 @@ +## +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '6.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompic', 'version': '2019b'} + +source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = [ + '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz +] + +dependencies = [ + ('CubeLib', '4.4.4'), + ('CubeWriter', '4.4.3'), + # Unwinding/sampling support (optional): + ('libunwind', '1.3.1'), + ('OPARI2', '2.0.5'), + ('OTF2', '2.2'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + [ + 'lib/libscorep_adapter_%s.%s' % (local_adapter, local_ext) + for local_adapter in local_adapters for local_ext in ('a', SHLIB_EXT) + ], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 998422138dcb4b1bd7338387b9cbd690201db960 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 15 Apr 2020 17:16:48 +0200 Subject: [PATCH 084/431] Allow http for tau --- easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb | 2 +- test/easyconfigs/easyconfigs.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb index 0286d5e26da..9e6087b9825 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['https://tau.uoregon.edu/pdt_releases/'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] sources = ['pdtoolkit-%(version)s.tar.gz'] checksums = [ '1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be', # pdtoolkit-3.25.tar.gz diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d7eae8d8f3a..7057b9e402f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -650,6 +650,8 @@ def check_https(self, changed_ecs): # https:// doesn't work, results in index page being downloaded instead # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) 'http://isl.gforge.inria.fr', + # https:// leads to File Not Found + 'http://tau.uoregon.edu/', ] http_regex = re.compile('http://[^"\'\n]+', re.M) From 1232dc74f5f567d0d410cdbb478265e061deff41 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 15 Apr 2020 17:53:29 +0200 Subject: [PATCH 085/431] adding easyconfigs: augur-7.0.2-intel-2019b-Python-3.7.4.eb, CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb, matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb, VCFtools-0.1.16-iccifort-2019.5.281.eb --- .../augur-7.0.2-intel-2019b-Python-3.7.4.eb | 130 ++++++++++++++++++ .../CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb | 41 ++++++ ...tplotlib-2.2.4-intel-2019b-Python-3.7.4.eb | 70 ++++++++++ .../VCFtools-0.1.16-iccifort-2019.5.281.eb | 30 ++++ 4 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..2f4ec30a35b --- /dev/null +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,130 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'augur' +version = '7.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nextstrain/augur' +description = "Pipeline components for real-time phylodynamic analysis" + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('Biopython', '1.75', versionsuffix), + ('SciPy-bundle', '2019.10', versionsuffix), + ('MAFFT', '7.453', '-with-extensions'), + ('IQ-TREE', '1.6.12'), + ('VCFtools', '0.1.16'), + ('RAxML', '8.2.12', '-hybrid-avx2'), + ('FastTree', '2.1.11'), + ('CVXOPT', '1.1.9', versionsuffix), + ('matplotlib', '2.2.4', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('bcbio-gff', '0.6.6', { + 'modulename': 'BCBio.GFF', + 'checksums': ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'], + }), + ('ConfigArgParse', '1.2.1', { + 'checksums': ['f30736dcd4e00455ffe3087454799ccb7f9b61d765492dd4b35bbcd62379db12'], + }), + ('cycler', '0.10.0', { + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('gitdb', '4.0.4', { + 'checksums': ['6f0ecd46f99bb4874e5678d628c3a198e2b4ef38daea2756a2bfd8df7dd5c1a5'], + }), + ('GitPython', '3.1.1', { + 'modulename': 'git', + 'checksums': ['6d4f10e2aaad1864bb0f17ec06a2c2831534140e5883c350d58b4e85189dab74'], + }), + ('importlib-metadata', '1.6.0', { + 'modulename': 'importlib_metadata', + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + }), + ('ipython-genutils', '0.2.0', { + 'modulename': 'ipython_genutils', + 'source_tmpl': 'ipython_genutils-%(version)s.tar.gz', + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('jupyter-core', '4.6.3', { + 'modulename': 'jupyter_core', + 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('kiwisolver', '1.2.0', { + 'checksums': ['247800260cd38160c362d211dcaf4ed0f7816afb5efe56544748b21d6ad6d17f'], + }), + ('nbformat', '5.0.5', { + 'checksums': ['f0c47cf93c505cb943e2f131ef32b8ae869292b5f9f279db2bafb35867923f69'], + }), + ('packaging', '20.3', { + 'checksums': ['3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3'], + }), + ('phylo-treetime', '0.7.5', { + 'modulename': 'treetime', + 'checksums': ['8e3b8003b75ca29b7e383d2ae0eb61dd47a6593eefdbb1e9995d93174b2ed576'], + }), + ('pyrsistent', '0.16.0', { + 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], + }), + ('PyYAML', '5.3.1', { + 'modulename': 'yaml', + 'checksums': ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'], + }), + ('ratelimiter', '1.2.0.post0', { + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('seaborn', '0.9.1', { + 'checksums': ['da33aa8c20a9a342ce73831d02831a10413f54a05471c7f31edf34f225d456ae'], + }), + ('smmap', '3.0.2', { + 'checksums': ['b46d3fc69ba5f367df96d91f8271e8ad667a198d5a28e215a6c3d9acd133a911'], + }), + ('snakemake', '5.10.0', { + 'checksums': ['a3fa8b12db84938c919996d61be66031bcb99c4b4d017278731324a6112b0d59'], + }), + ('toposort', '1.5', { + 'checksums': ['dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd'], + }), + ('traitlets', '4.3.3', { + 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/nextstrain/augur/archive/'], + 'use_pip_extras': 'full', + 'checksums': ['bf520dfc7fe2bf72e12c8de25cd97ca84686345fbb1c4a3456b060500c9c25b3'], + }), +] + +sanity_check_paths = { + 'files': ['bin/augur'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ["augur --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..dc028da0624 --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,41 @@ +easyblock = "PythonPackage" + +name = 'CVXOPT' +version = '1.1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.1.9-fix-setup-py.patch'] +checksums = [ + '8f157e7397158812cabd340b68546f1baa55a486ed0aad8bc26877593dc2983d', # cvxopt-1.1.9.tar.gz + '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3', # CVXOPT-1.1.9-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), + ('GSL', '2.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE ' + +installopts = '--no-binary cvxopt' + +sanity_check_commands = ['nosetests'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..c439a318ad9 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('subprocess32', '3.5.4', { + 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('backports.functools_lru_cache', '1.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], + 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], + }), + ('kiwisolver', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], + }), +] + +postinstallcmds = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', +] + +sanity_pip_check = True + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-iccifort-2019.5.281.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..ff7145a5486 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-iccifort-2019.5.281.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +dependencies = [ + ('Perl', '5.30.0'), + ('HTSlib', '1.10.2'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From 258442e48e0d0ed1d07c4ffa8881677b34969418 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 15 Apr 2020 19:38:18 +0200 Subject: [PATCH 086/431] FusionCatcher-1.20: use common sources and start_dir, clarify installation instructions for the database and add aligner using bowtie2 --- ...onCatcher-1.20-foss-2019b-Python-2.7.16.eb | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb index 4c2dc45f594..328e19e1981 100644 --- a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb @@ -34,21 +34,22 @@ dependencies = [ local_bbmap_makefile = 'makefile.%s' % {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +default_component_specs = { + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'start_dir': '%(namelower)s-%(version)s', +} + components = [ (name, version, { 'easyblock': 'Tarball', 'source_urls': [GITHUB_SOURCE], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['4c66dbd7be64aaf52ab1f02278f06d9a8082b7f3f30a8045a50b4899e22a0385'], - 'start_dir': '%(namelower)s-%(version)s', }), # FusionCatcher requires a fork of seqtk with features not available upstream ('seqtk', '1.2-r101c', { 'easyblock': 'MakeCp', 'source_urls': ['http://github.com/ndaniel/seqtk/archive'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['4a57fbe828eccaa4f0122c84bf9c4c5409a024ad9deace31ec7bee6d25cf5e49'], - 'start_dir': '%(name)s-%(version)s', 'files_to_copy': [(['seqtk'], 'tools/%(name)s')], }), # FusionCatcher requires this very specific version of BBMap @@ -64,14 +65,15 @@ components = [ }), ] -# Set paths in the configuration file +# Set paths and options in the configuration file postinstallcmds = [ 'sed -i "s|python = /usr/bin/|python = $EBROOTPYTHON/bin/|g" %(installdir)s/etc/configuration.cfg', 'sed -i "s|java = /usr/bin/|python = $EBROOTJAVA/bin/|g" %(installdir)s/etc/configuration.cfg', 'sed -i "s|paralell/src|parallel/bin|g" %(installdir)s/etc/configuration.cfg', + 'sed -i "s|aligners = blat,star|aligners = blat,star,bowtie2|g" %(installdir)s/etc/configuration.cfg', ] -# Create symlinks in installation dir to dependencies from EB +# Create symlinks in tools directory to dependencies from EB postinstallcmds += [ 'ln -s $EBROOT%s %%(installdir)s/tools/%s' % (d, d.lower()) for d in [ 'BLAT', 'BOWTIE', 'BOWTIE2', 'BWA', 'PARALLEL', 'PICARD', 'PIGZ', 'STAR', 'VELVET' @@ -88,13 +90,11 @@ postinstallcmds += [ ] ] -# Link the required Ensembl database -# Database can be created after install with `fusioncatcher-build -g homo_sapiens -o /path/to/human_v98` -# More information at https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md -# postinstallcmds += [ -# 'ln -s /path/to/database/human_v98 %(installdir)s/data/human_v98', -# 'cd %(installdir)s/data && ln -s human_v98 current', -# ] +# Link the required Ensembl database: it can be either downloaded (>16GB) or built on-site +# - Download: database download script available at %(installdir)s/data/download-human-db.sh +# path to downloaded data folder can be set with '--data' option in fusioncatcher +# - Build: database can be created after install with `fusioncatcher-build -g homo_sapiens -o /path/to/human_v98` +# more information at https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md # Tests need 16 cores and 64 GB of RAM as well as the Ensembl database # postinstallcmds += ['%(installdir)s/test/test.sh'] From 609443687b13e264d509f43d8b1924deb05d1afb Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 16 Apr 2020 11:01:41 +1000 Subject: [PATCH 087/431] Update easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb index 20c16b11b9c..0430235e6fa 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb @@ -16,4 +16,6 @@ dependencies = [ ('ncurses', '6.1'), ] +configopts = '--with-tcsetpgrp' # needed to build in non-login shells + moduleclass = 'tools' From 67f35f1ce622d42fc320416dd9c77e28c81965d4 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 16 Apr 2020 11:27:30 +1000 Subject: [PATCH 088/431] Update easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb index 0430235e6fa..babb3ea8fe8 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb @@ -18,4 +18,9 @@ dependencies = [ configopts = '--with-tcsetpgrp' # needed to build in non-login shells +sanity_check_paths = { + 'files': ['bin/zsh'], + 'dirs': ['lib/zsh/%(version)s', 'share'], +} + moduleclass = 'tools' From a30a78b0a628612137b00e06626fb337688af467 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 09:56:56 +0200 Subject: [PATCH 089/431] fixed hardcoded requirements to allow newer versions of matplotlib and cvxopt --- .../augur-7.0.2-intel-2019b-Python-3.7.4.eb | 9 ++- ... CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb} | 12 ++-- ...tplotlib-2.2.4-intel-2019b-Python-3.7.4.eb | 70 ------------------- 3 files changed, 13 insertions(+), 78 deletions(-) rename easybuild/easyconfigs/c/CVXOPT/{CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb => CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb} (79%) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index 2f4ec30a35b..f8c1e92a144 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -21,8 +21,8 @@ dependencies = [ ('VCFtools', '0.1.16'), ('RAxML', '8.2.12', '-hybrid-avx2'), ('FastTree', '2.1.11'), - ('CVXOPT', '1.1.9', versionsuffix), - ('matplotlib', '2.2.4', versionsuffix), + ('CVXOPT', '1.2.4', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), ] use_pip = True @@ -118,6 +118,11 @@ exts_list = [ 'source_urls': ['https://github.com/nextstrain/augur/archive/'], 'use_pip_extras': 'full', 'checksums': ['bf520dfc7fe2bf72e12c8de25cd97ca84686345fbb1c4a3456b060500c9c25b3'], + # Change augur strict dependency on matplotlib and cvxopt. Newer versions can be used. + 'preinstallopts': """ + sed -i'' 's/"matplotlib >=2.0, ==2.*",/"matplotlib >=2.0",/' setup.py && + sed -i'' 's/"cvxopt >=1.1.9, ==1.1.*",/"cvxopt >=1.1.9",/' setup.py && + """, }), ] diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb similarity index 79% rename from easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb index dc028da0624..0cb58787e2c 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.1.9-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb @@ -1,7 +1,7 @@ easyblock = "PythonPackage" name = 'CVXOPT' -version = '1.1.9' +version = '1.2.4' versionsuffix = '-Python-%(pyver)s' homepage = 'http://cvxopt.org' @@ -15,11 +15,11 @@ toolchainopts = {'pic': True} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['CVXOPT-1.1.9-fix-setup-py.patch'] -checksums = [ - '8f157e7397158812cabd340b68546f1baa55a486ed0aad8bc26877593dc2983d', # cvxopt-1.1.9.tar.gz - '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3', # CVXOPT-1.1.9-fix-setup-py.patch -] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +# checksums = [ +# '8f157e7397158812cabd340b68546f1baa55a486ed0aad8bc26877593dc2983d', # cvxopt-1.1.9.tar.gz +# '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3', # CVXOPT-1.1.9-fix-setup-py.patch +# ] dependencies = [ ('Python', '3.7.4'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb deleted file mode 100644 index c439a318ad9..00000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2019b-Python-3.7.4.eb +++ /dev/null @@ -1,70 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'matplotlib' -version = '2.2.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'intel', 'version': '2019b'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.7.4'), - ('SciPy-bundle', '2019.10', versionsuffix), - ('libpng', '1.6.37'), - ('freetype', '2.10.1'), - ('Tkinter', '%(pyver)s'), -] - -use_pip = True - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('subprocess32', '3.5.4', { - 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], - 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], - }), - ('backports.functools_lru_cache', '1.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], - 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], - }), - ('kiwisolver', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], - 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], - }), -] - -postinstallcmds = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', -] - -sanity_pip_check = True - -sanity_check_commands = [ - """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, - "python -c 'from mpl_toolkits.mplot3d import Axes3D'", -] - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' From 05cdef1951516b8d78e565ff9826e0647d106489 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 10:14:10 +0200 Subject: [PATCH 090/431] added checksums --- .../c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb index 0cb58787e2c..3836ff1afa6 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb @@ -16,10 +16,10 @@ toolchainopts = {'pic': True} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] -# checksums = [ -# '8f157e7397158812cabd340b68546f1baa55a486ed0aad8bc26877593dc2983d', # cvxopt-1.1.9.tar.gz -# '89058d53c55dcdc94a9b7a6ea8c6a6e78a693210d1d27a4178f68926ae5099e3', # CVXOPT-1.1.9-fix-setup-py.patch -# ] +checksums = [ + 'fa5ced96d71e4c3e6d50735e2ac4b8cf125c388cd77b1c5937febedb5f3a2fc1', # cvxopt-1.2.4.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] dependencies = [ ('Python', '3.7.4'), From 1afcf84310054fdfa60ea8b67b02baaa9645e315 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 16 Apr 2020 11:03:06 +0200 Subject: [PATCH 091/431] add perl as a builddependency for autoconf needed for https://github.com/easybuilders/easybuild-easyconfigs/issues/8704 --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb index 2dc65b675b7..181f60b0e48 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb @@ -22,6 +22,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] builddependencies = [ ('binutils', '2.32'), + ('Perl', '5.30.0'), ] dependencies = [ From 0eac081429ee61f5b74070ddfc4788a12ba4afd7 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 16 Apr 2020 11:05:51 +0200 Subject: [PATCH 092/431] Update Autoconf-2.69-GCCcore-8.3.0.eb fix indentation --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb index 181f60b0e48..c98e7f30548 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb @@ -22,7 +22,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] builddependencies = [ ('binutils', '2.32'), - ('Perl', '5.30.0'), + ('Perl', '5.30.0'), ] dependencies = [ From 0f53c7333930318e183eb632a2fc5324f48b41ea Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 16 Apr 2020 11:26:30 +0200 Subject: [PATCH 093/431] same for automake as for autoconf --- .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb index cf2b65896b1..5c5492891c0 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb @@ -27,6 +27,7 @@ checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] builddependencies = [ ('binutils', '2.32'), + ('Perl', '5.30.0'), ] dependencies = [ From 3002e78a912308f50102acd2c260f0d05e76051c Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 16 Apr 2020 11:28:22 +0200 Subject: [PATCH 094/431] use https for automake homepage --- .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb index 5c5492891c0..0d5f3f9d2c6 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Automake' version = '1.16.1' -homepage = 'http://www.gnu.org/software/automake/automake.html' +homepage = 'https://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" From 83b90bb08bd894d8d0da1bf8405a1b1ee376d694 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 16 Apr 2020 11:28:50 +0200 Subject: [PATCH 095/431] use https for autoconf homepage --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb index c98e7f30548..6f0873d76b5 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Autoconf' version = '2.69' -homepage = 'http://www.gnu.org/software/autoconf/' +homepage = 'https://www.gnu.org/software/autoconf/' description = """ Autoconf is an extensible package of M4 macros that produce shell scripts From 383ad5de6526fdb47eab2328d3b7b3c8e5b4aa77 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 11:40:21 +0200 Subject: [PATCH 096/431] fixed errors, added sanity_checks --- .../augur-7.0.2-intel-2019b-Python-3.7.4.eb | 19 ++++++++++++++++++- .../CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb | 8 ++++---- 2 files changed, 22 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index f8c1e92a144..7ef373d61ff 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -130,6 +130,23 @@ sanity_check_paths = { 'files': ['bin/augur'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["augur --help"] +sanity_check_commands = [ + "augur --help", + + # Check if cvxopt imports in augur are valid + "python -c 'from cvxopt import matrix, solvers'", + + # Check if matplotlib imports in augur are valid + # scripts/plot_tree.py + """python -c ' +import matplotlib as mpl +mpl.use("Agg") +from matplotlib import gridspec +import matplotlib.pyplot as plt +from matplotlib.collections import LineCollection +'""", + # scripts/swap_colors.py + "python -c 'from matplotlib.colors import LinearSegmentedColormap, to_hex'", +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb index 3836ff1afa6..641cd7e6584 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb @@ -1,10 +1,10 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'CVXOPT' version = '1.2.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cvxopt.org' +homepage = 'https://cvxopt.org' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. @@ -32,9 +32,9 @@ use_pip = True sanity_pip_check = True preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' -preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' -installopts = '--no-binary cvxopt' +installopts = ' --no-binary cvxopt' sanity_check_commands = ['nosetests'] From 640ac223587a06965a8bce3fdad7e010a265260b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 11:58:05 +0200 Subject: [PATCH 097/431] adding easyconfigs: Python-3.8.2-GCCcore-9.3.0.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb | 38 +++ .../Automake/Automake-1.16.1-GCCcore-9.3.0.eb | 41 +++ .../Autotools-20180311-GCCcore-9.3.0.eb | 24 ++ .../b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb | 28 ++ .../g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb | 35 +++ .../l/libffi/libffi-3.3-GCCcore-9.3.0.eb | 30 ++ .../libreadline-8.0-GCCcore-9.3.0.eb | 41 +++ .../l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb | 32 ++ .../n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 41 +++ .../p/Python/Python-3.8.2-GCCcore-9.3.0.eb | 296 ++++++++++++++++++ .../s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb | 47 +++ .../t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb | 41 +++ .../x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 33 ++ 13 files changed, 727 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..1e2780e6f96 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..89abe4f1110 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.1' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..04460cc610a --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-9.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20180311' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.16.1'), # 20180311 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..188fa77e175 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-1.0.6-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..1cff3d1972e --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.0' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.34'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..246ea276b29 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-9.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.3' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/%(name)s/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/%(name)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['72fba7922703ddfa7a028d513ac15a85c8d54c8d67f55fa5a4802885dc652056'] + +builddependencies = [ + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8971e851e81 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.0' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461'] + +builddependencies = [ + ('binutils', '2.34'), +] +dependencies = [ + ('ncurses', '6.2'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..da5ae743abb --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d1e45e0229f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.2' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] + +builddependencies = [('binutils', '2.34')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d59cda2a045 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb @@ -0,0 +1,296 @@ +name = 'Python' +version = '3.8.2' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561'] + +dependencies = [ + ('binutils', '2.34'), # required for pip install that involves compilation + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.31.1'), + ('XZ', '5.2.5'), + ('GMP', '6.2.0'), # required for pycrypto + ('libffi', '3.3'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) + # ('OpenSSL', '1.1.1e'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# symlink 'pip' command to 'pip3' that is included with Python installation +# required so we can update pip to version included in extensions, using pip +installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" + + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated Feb 22nd 2020 +exts_list = [ + ('pip', '20.0.2', { + 'use_pip': False, + 'checksums': ['7db0c8ea4c7ea51c8049640e8e6e7fde949de672bfa4949920675563a5a6967f'], + }), + ('setuptools', '45.2.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['89c6e6011ec2f6d57d43a3f9296c4ef022c2cbf49bab26b407fe67992ae3397f'], + }), + ('wheel', '0.34.2', { + 'checksums': ['8788e9155fe14f54164c1b9eb0a319d98ef02c160725587ad60f14ddc57b6f96'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.4.4', { + 'checksums': ['139d2625547dbfa5fb0b81daebb39601c478c21956dc57e2e07b74450a8c506b'], + }), + ('Cython', '0.29.15', { + 'checksums': ['60d859e1efa5cc80436d58aecd3718ff2e74b987db0518376046adedba97ac30'], + }), + ('six', '1.14.0', { + 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], + }), + ('toml', '0.10.0', { + 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], + }), + ('setuptools_scm', '3.5.0', { + 'checksums': ['5bdf21a05792903cafe7ae0c9501182ab52497614fa6b1750d9dbae7b60c1a87'], + }), + ('python-dateutil', '2.8.1', { + 'modulename': 'dateutil', + 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], + }), + ('decorator', '4.4.1', { + 'checksums': ['54c38050039232e1db4ad7375cfce6748d7b41c29e95a081c8a6d2c30364a2ce'], + }), + ('liac-arff', '2.4.0', { + 'modulename': 'arff', + 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.15', { + 'checksums': ['8f12ac317f8a1318efa75757ef0a651abe12e51fc1af8838fb91079445227277'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.3.0', { + 'checksums': ['5a215cb8dc12f892244e3a113fe05397ee23c5c4ca7a69cd6e69811755efc42d'], + }), + ('idna', '2.9', { + 'checksums': ['7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb'], + }), + ('pycparser', '2.19', { + 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], + }), + ('cffi', '1.14.0', { + 'checksums': ['2d384f4a127a15ba701207f7639d94106693b6cd64173d6c8988e2c25f3ac2b6'], + }), + ('cryptography', '2.8', { + 'checksums': ['3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.3.0', { + 'modulename': 'nacl', + 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + }), + ('bcrypt', '3.1.7', { + 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], + }), + ('paramiko', '2.7.1', { + 'checksums': ['920492895db8013f6cc0179293147f830b8c7b21fdfc839b6bad760c27459d9f'], + }), + ('pyparsing', '2.4.6', { + 'checksums': ['4c830582a84fb022400b85429791bc551f1f4871c33f23e44f353119e92f969f'], + }), + ('netifaces', '0.10.9', { + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.7.19', { + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('mock', '4.0.1', { + 'checksums': ['2a572b715f09dd2f0a583d8aeb5bb67d7ed7a8fd31d193cf1227a99c16a67bc3'], + }), + ('pytz', '2019.3', { + 'checksums': ['b02c06db6cf09c12dd25137e563b31700d3b80fcc4ad23abb7a315f2789819be'], + }), + ('bitstring', '3.1.6', { + 'checksums': ['c97a8e2a136e99b523b27da420736ae5cb68f83519d633794a6a11192f69f8bf'], + }), + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('distlib', '0.3.0', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['2e166e231a26b36d6dfe35a48c4464346620f8645ed0ace01ee31822b288de21'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('virtualenv', '20.0.5', { + 'checksums': ['531b142e300d405bb9faedad4adbeb82b4098b918e35209af2adef3129274aae'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.14.1', { + 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], + }), + ('chardet', '3.0.4', { + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2019.11.28', { + 'checksums': ['25b64c7da4cd7479594d035c08c2d809eb4aab3a26e5a990ea98cc450c320f1f'], + }), + ('urllib3', '1.25.8', { + 'checksums': ['87716c2d2a7121198ebcb7ce7cccf6ce5e9ba539041cfbaeecfb641dc0bf6acc'], + }), + ('requests', '2.23.0', { + 'checksums': ['b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.9', { + 'checksums': ['d80a948f91f78d08f789b0a7c3fb2bd9a34ad625f5ce88c262a6c91189a4abb9'], + }), + ('tabulate', '0.8.6', { + 'checksums': ['5470cc6687a091c7042cee89b2946d9235fe9f6d49c193a4ae2ac7bf386737c8'], + }), + ('ujson', '1.35', { + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), + ('atomicwrites', '1.3.0', { + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('py', '1.8.1', { + 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], + }), + ('importlib_metadata', '1.5.0', { + 'checksums': ['06f5b3a99029c7134207dd882428a66992a9de2bef7c2b699b5641f9886c3302'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '8.2.0', { + 'checksums': ['b1ddb932186d8a6ac451e1d95844b382f55e12686d51ca0c68b6f61f2ab7a507'], + }), + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('wcwidth', '0.1.8', { + 'checksums': ['f28b3e8a6483e5d49e7f8949ac1a78314e740333ae305b4ba5defd3e74fb37a8'], + }), + ('pytest', '5.3.5', { + 'checksums': ['0d5fe9189a148acc3c3eb2ac8e1ac0742cb7618c084f3d228baaec0c254b318d'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.1', { + 'checksums': ['93187ffbc7808079673ef52771baa950426fd664d3aad1d0fa3e95644360e250'], + }), + ('packaging', '20.1', { + 'checksums': ['e665345f9eef0c621aa0bf2f8d78cf6d21904eef16a93f020240b704a57f1334'], + }), + ('sphinxcontrib-websupport', '1.2.0', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['bad3fbd312bc36a31841e06e7617471587ef642bdacdbdddaa8cc30cf251b5ea'], + }), + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], + }), + ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('sphinxcontrib-applehelp', '1.0.1', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897'], + }), + ('sphinxcontrib-devhelp', '1.0.1', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['6c64b077937330a9128a4da74586e8c2130262f014689b4b89e2d08ee7294a34'], + }), + ('sphinxcontrib-htmlhelp', '1.0.3', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib-qthelp', '1.0.2', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['79465ce11ae5694ff165becda529a600c754f4bc459778778c7017374d4d406f'], + }), + ('sphinxcontrib-serializinghtml', '1.1.3', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['c0efb33f8052c04fd7a26c0a07f1678e8512e0faec19f4aa8f2473a8b81d5227'], + }), + ('Sphinx', '2.4.2', { + 'checksums': ['525527074f2e0c2585f68f73c99b4dc257c34bbe308b27f5f8c7a6e20642742f'], + }), + ('Click', '7.0', { + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('psutil', '5.7.0', { + 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..32f6e2c4fd3 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb @@ -0,0 +1,47 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: https://hpcbios.readthedocs.org/en/latest/ +# # + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.31.1' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/2019/'] +sources = ['%(namelower)s-autoconf-%(version_major)s290000.tar.gz'] +checksums = ['8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b'] + +builddependencies = [ + ('binutils', '2.34'), +] +dependencies = [ + ('libreadline', '8.0'), + ('Tcl', '8.6.10'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..6bccbe04ae5 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['5196dbf6638e3df8d5c87b5815c8c2b758496eb6f0e41446596c9a4e638d87ed'] + +builddependencies = [ + ('binutils', '2.34'), +] +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..fa1a3854e24 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.5' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.20.1', '', True), + ('binutils', '2.34'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' From 006219fc876085f1170d55c5c7009d4cb33fbf64 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 16 Apr 2020 12:02:32 +0200 Subject: [PATCH 098/431] Fix style --- .../easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb index d2df82c6b38..75ffc099a04 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb @@ -47,11 +47,12 @@ local_adapters = [ 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' ] sanity_check_paths = { - 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h'] + - [ - 'lib/libscorep_adapter_%s.%s' % (local_adapter, local_ext) - for local_adapter in local_adapters for local_ext in ('a', SHLIB_EXT) - ], + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + [ + 'lib/libscorep_adapter_%s.%s' % (local_adapter, local_ext) + for local_adapter in local_adapters for local_ext in ('a', SHLIB_EXT) + ], 'dirs': [], } sanity_check_commands = ['scorep-config --help'] From dbe40f8ec08f278920781143a9aa29be218af6e5 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 12:09:11 +0200 Subject: [PATCH 099/431] fixed whitespaces? --- .../a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index 7ef373d61ff..34a6f66a05f 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -119,9 +119,8 @@ exts_list = [ 'use_pip_extras': 'full', 'checksums': ['bf520dfc7fe2bf72e12c8de25cd97ca84686345fbb1c4a3456b060500c9c25b3'], # Change augur strict dependency on matplotlib and cvxopt. Newer versions can be used. - 'preinstallopts': """ - sed -i'' 's/"matplotlib >=2.0, ==2.*",/"matplotlib >=2.0",/' setup.py && - sed -i'' 's/"cvxopt >=1.1.9, ==1.1.*",/"cvxopt >=1.1.9",/' setup.py && + 'preinstallopts': """sed -i'' 's/"matplotlib >=2.0, ==2.*",/"matplotlib >=2.0",/' setup.py &&""" + + """sed -i'' 's/"cvxopt >=1.1.9, ==1.1.*",/"cvxopt >=1.1.9",/' setup.py && """, }), ] @@ -130,14 +129,11 @@ sanity_check_paths = { 'files': ['bin/augur'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +# Check if cvxopt and matplotlib imports in augur are valid +# Check if imports in augur are valid sanity_check_commands = [ "augur --help", - - # Check if cvxopt imports in augur are valid "python -c 'from cvxopt import matrix, solvers'", - - # Check if matplotlib imports in augur are valid - # scripts/plot_tree.py """python -c ' import matplotlib as mpl mpl.use("Agg") @@ -145,7 +141,6 @@ from matplotlib import gridspec import matplotlib.pyplot as plt from matplotlib.collections import LineCollection '""", - # scripts/swap_colors.py "python -c 'from matplotlib.colors import LinearSegmentedColormap, to_hex'", ] From 3472a93de9bcafddb0b3611e651f0efb7e75e55e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 13:11:41 +0200 Subject: [PATCH 100/431] adding easyconfigs: Perl-5.30.2-GCCcore-9.3.0.eb --- .../e/expat/expat-2.2.9-GCCcore-9.3.0.eb | 33 + .../libreadline-8.0-GCCcore-9.3.0.eb | 41 + .../n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 41 + .../p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 1707 +++++++++++++++++ 4 files changed, 1822 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b67f00edf41 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.9-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.9' + +homepage = 'https://libexpat.github.io' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f1063084dc4302a427dabcca499c8312b3a32a29b7d2506653ecc8f950a9a237'] + +builddependencies = [('binutils', '2.34')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8971e851e81 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.0' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461'] + +builddependencies = [ + ('binutils', '2.34'), +] +dependencies = [ + ('ncurses', '6.2'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d1e45e0229f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.2' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] + +builddependencies = [('binutils', '2.34')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c6295da16ae --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -0,0 +1,1707 @@ +name = 'Perl' +version = '5.30.2' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('zlib', '1.2.11'), # for Net::SSLeay + ('expat', '2.2.9'), # for XML::Parser + ('ncurses', '6.2'), # for Term::ReadLine::Gnu + ('libreadline', '8.0'), # for Term::ReadLine::Gnu +] + +# OpenSSL is required for Net::SSLeay +osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# !! order of extensions is important !! +# extensions updated on Sept 13th 2019 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.42', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['0fd90d4efea82d6e262e6933759e85d27cbcfa4091b14bf4042ae20bab528e53'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0'], + }), + ('Test::Warnings', '0.029', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b55214ea50395f1ae14ac504dd3d0d21580a92c558e8049cbe7b3ac42add1792'], + }), + ('File::ShareDir', '1.116', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['59d90bfdf98c4656ff4173e62954ea8cf0de66565e35d108ecd7050596cb8328'], + }), + ('File::ShareDir::Install', '0.13', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], + }), + ('DateTime::Locale', '1.25', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['aa79746bd488b32aa4dbccccd05f1e5505642be013d8064a5d6f8a76a3c45d0b'], + }), + ('DateTime::TimeZone', '2.38', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0e5c99ef22471f4d262ac590ce5ce8177094d7a92f380d8eea6219f5a12dc0cd'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('Module::Build', '0.4231', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7e0f4c692c1740c1ac84ea14d7ea3d8bc798b2fb26c09877229e04f430b2b717'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': 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'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Time::HiRes', '1.9760', { + 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['2cb898bff42bc10024e0a3252c79e13a2eb7a8a5fb3367bb60583b576a11702b'], + }), + ('Term::ReadLine::Gnu', '1.36', { + 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], + 'checksums': ['9a08f7a4013c9b865541c10dbba1210779eb9128b961250b746d26702bab6925'], + }), + ('ExtUtils::MakeMaker', '7.44', { + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['52a18f8271250faf5f3527499dd2b78d3b4fd3b064408d0cfdda9a3538887188'], + }), + ('List::Util', '1.54', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['a6eda0eb8fd69890c2369ad12c1fd1b8aab5b38793cac3688d7fc402c630bf79'], + }), + ('Module::CoreList', '5.20200314', { + 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['21566e741e7eb29e3ec44f059cdce8dda014bcada59a85cff91148f88dc46de9'], + }), + ('Module::Metadata', '1.000037', { + 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8d5a74c1b07e145edda254602fedf19c0dd0c2d9688a370afdaff89c32cba629'], + }), + ('Params::Check', '0.38', { + 'source_tmpl': 'Params-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], + }), + ('Locale::Maketext::Simple', '0.21', { + 'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'], + }), + ('Perl::OSType', '1.010', { + 'source_tmpl': 'Perl-OSType-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['e7ed4994b5d547cb23aadb84dc6044c5eb085d5a67a6c5624f42542edd3403b2'], + }), + ('IPC::Cmd', '1.04', { + 'source_tmpl': 'IPC-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d110a0f60e35c65721454200f0d2f0f8965529a2add9649d1fa6f4f9eccb6430'], + }), + ('Pod::Escapes', '1.07', { + 'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], + }), + ('if', '0.0608', { + 'source_tmpl': 'if-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], + }), + ('Test', '1.26', { + 'source_tmpl': 'Test-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], + }), + ('ExtUtils::Constant', '0.25', { + 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], + }), + ('ExtUtils::CBuilder', '0.280234', { + 'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'], + 'checksums': ['d80095ea1f28b4908cbedacead63f61f762472bba898281449dad782deecf1c3'], + }), + ('Carp::Heavy', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('IO::Handle', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('IO::Seekable', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('Pod::Simple', '3.40', { + 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], + 'checksums': ['063a8cb9d8abd84fd64c3e9581addf96a6b0f77a2048a1846c3a6b14269a040d'], + }), + ('IO::File', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('IO::Select', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('IO::Socket', '1.42', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + }), + ('Socket', '2.029', { + 'source_tmpl': 'Socket-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['3a8d1710a28bf5d7bc46737e43e83657ed4b1c1842efc4cde06c9dd3f6831f06'], + }), + ('Time::Local', '1.30', { + 'source_tmpl': 'Time-Local-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c7744f6b2986b946d3e2cf034df371bee16cdbafe53e945abb1a542c4f8920cb'], + }), + ('Storable', '3.15', { + 'source_tmpl': 'Storable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['fc3dad06cb2e6fc86a2f2abc5b5491d9da328ca3e6b6306559c224521db174da'], + }), + ('ExtUtils::ParseXS', '3.35', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['41def0511278a2a8ba9afa25ccab45b0453f75e7fd774e8644b5f9a57cc4ee1c'], + }), + ('Pod::Man', '4.14', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['7af1c41de34b2e4dbff700a29d7387549c2b6cf16142214450c924707ddb0f82'], + }), + ('Test::More', '1.302172', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['7388768f04128294a0e24c553eefbd2a464464617a8c19dfc21538ad5f4334fc'], + }), + ('Module::Load', '0.34', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['7f5b0c4d3cc8ba867639bff61ad857a940970ea246dd3b0a6729dd7fc84059f3'], + }), + ('Module::Load::Conditional', '0.70', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['ca705e80e3da32b15d375b26fe86c5f716c8ee5964f3e1c5a1b5bbc7bb4766e8'], + }), + ('parent', '0.238', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['38f58fdef3e28a194c9c8d0dc5d02672faf93c069f40c5bcb1fabeadbbc4d2d1'], + }), + ('Net::Domain', '3.11', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['2fab1e4d6e565c77f6e845368790de65cb2f966fcd9bb56a41d0e7b5851a52d3'], + }), + ('Scalar::Util', '1.54', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['a6eda0eb8fd69890c2369ad12c1fd1b8aab5b38793cac3688d7fc402c630bf79'], + }), + ('Text::ParseWords', '3.30', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['85e0238179dd43997e58c66bd51611182bc7d533505029a2db0d3232edaff5e8'], + }), + ('Encode', '3.04', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['2a04dc334846915bdb52ef03422f4f47ce588d2edf4b8ae4e7e442748e7ae09a'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Data::Dumper', '2.173', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + }), + ('Cwd', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('ExtUtils::CppGuess', '0.21', { + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['ff629178321a1e591b83f809712593eae4408a413aa448654bce59b156f24153'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('URI::Escape', '3.31', { + 'source_tmpl': 'URI-1.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b2c98e1d50d6f572483ee538a6f4ccc8d9185f91f0073fd8af7390898254413e'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), +] + +moduleclass = 'lang' From bb908d3f5ecfca91c3c1d39d5f561094ec236bd8 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 13:28:28 +0200 Subject: [PATCH 101/431] fixed whitespaces now? --- .../easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index 34a6f66a05f..76884130712 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -120,7 +120,7 @@ exts_list = [ 'checksums': ['bf520dfc7fe2bf72e12c8de25cd97ca84686345fbb1c4a3456b060500c9c25b3'], # Change augur strict dependency on matplotlib and cvxopt. Newer versions can be used. 'preinstallopts': """sed -i'' 's/"matplotlib >=2.0, ==2.*",/"matplotlib >=2.0",/' setup.py &&""" + - """sed -i'' 's/"cvxopt >=1.1.9, ==1.1.*",/"cvxopt >=1.1.9",/' setup.py && + """sed -i'' 's/"cvxopt >=1.1.9, ==1.1.*",/"cvxopt >=1.1.9",/' setup.py && """, }), ] From 275de52bb85602bda05117b46076613d0ba22bf5 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 13:46:39 +0200 Subject: [PATCH 102/431] fixed remarks --- .../a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index 76884130712..07266e3d30f 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -30,6 +30,9 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} +local_augur_preinstallopts = """sed -i'' 's/"matplotlib >=2.0,.*/"matplotlib >=2.0",/' setup.py && """ +local_augur_preinstallopts += """sed -i'' 's/"cvxopt >=1.1.9,.*/"cvxopt >=1.1.9",/' setup.py && """ + exts_list = [ ('appdirs', '1.4.3', { 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], @@ -119,9 +122,7 @@ exts_list = [ 'use_pip_extras': 'full', 'checksums': ['bf520dfc7fe2bf72e12c8de25cd97ca84686345fbb1c4a3456b060500c9c25b3'], # Change augur strict dependency on matplotlib and cvxopt. Newer versions can be used. - 'preinstallopts': """sed -i'' 's/"matplotlib >=2.0, ==2.*",/"matplotlib >=2.0",/' setup.py &&""" + - """sed -i'' 's/"cvxopt >=1.1.9, ==1.1.*",/"cvxopt >=1.1.9",/' setup.py && - """, + 'preinstallopts': local_augur_preinstallopts, }), ] From b63f1e67792431b86ac4f188007e03c81d7ac5b8 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 14:02:37 +0200 Subject: [PATCH 103/431] Perl: add module LWP::UserAgent to v5.30 --- .../p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb index b14a746e798..417ce82c1b6 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb @@ -1637,11 +1637,36 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], 'checksums': ['7af1c41de34b2e4dbff700a29d7387549c2b6cf16142214450c924707ddb0f82'], }), + ('LWP::UserAgent', '6.43', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], + }), + ('Mozilla::CA', '20180117', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], + 'checksums': ['f2cc9fbe119f756313f321e0d9f1fac0859f8f154ac9d75b1a264c1afdf4e406'], + }), + ('Net::HTTPS', '6.19', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['52b76ec13959522cae64d965f15da3d99dcb445eddd85d2ce4e4f4df385b2fc4'], + }), ('Test::More', '1.302171', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN/'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('LWP::Protocol::https', '6.07', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['522cc946cf84a1776304a5737a54b8822ec9e79b264d0ba0722a70473dbfb9e7'], + }), ('Module::Load', '0.34', { 'source_tmpl': 'Module-Load-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], From e8c50ca21568f22a74e36224b03fed72a1313d84 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 16 Apr 2020 14:03:27 +0200 Subject: [PATCH 104/431] fixed remarks --- ... => ARAGORN-1.2.38-iccifort-2019.5.281.eb} | 4 +- .../Bio-EUtilities-1.76-GCCcore-8.3.0.eb | 68 +++++++++--------- .../LWP-Protocol-https-6.07-GCCcore-8.3.0.eb | 72 ------------------- .../swissknife-1.79-GCCcore-8.3.0.eb | 30 +++----- 4 files changed, 43 insertions(+), 131 deletions(-) rename easybuild/easyconfigs/a/ARAGORN/{ARAGORN-1.2.38-GCCcore-8.3.0.eb => ARAGORN-1.2.38-iccifort-2019.5.281.eb} (90%) delete mode 100644 easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-iccifort-2019.5.281.eb similarity index 90% rename from easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-iccifort-2019.5.281.eb index 41b573c7cfd..ac2d77a84a7 100644 --- a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.38-iccifort-2019.5.281.eb @@ -12,14 +12,12 @@ version = '1.2.38' homepage = 'http://mbio-serv2.mbioekol.lu.se/ARAGORN/' description = "a program to detect tRNA genes and tmRNA genes in nucleotide sequences" -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} source_urls = ['http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/'] sources = ['%(namelower)s%(version)s.tgz'] checksums = ['4b84e3397755fb22cc931c0e7b9d50eaba2a680df854d7a35db46a13cecb2126'] -builddependencies = [('binutils', '2.32')] - cmds_map = [(".*", "$CC $CFLAGS -o aragorn aragorn%(version)s.c")] files_to_copy = [ diff --git a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb index 5cf24ec9c01..ddfd6cf5d09 100644 --- a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb @@ -21,48 +21,48 @@ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ - ('ExtUtils::MakeMaker', '7.44', { - 'source_tmpl': 'ExtUtils-MakeMaker-7.44.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - 'checksums': ['52a18f8271250faf5f3527499dd2b78d3b4fd3b064408d0cfdda9a3538887188'], - }), - ('IO::Handle', '1.42', { - 'source_tmpl': 'IO-1.42.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], - 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], - }), - ('Test::More', '0', { - 'source_tmpl': 'Test-Simple-1.302171.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], - }), + # ('ExtUtils::MakeMaker', '7.44', { + # 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + # 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + # 'checksums': ['52a18f8271250faf5f3527499dd2b78d3b4fd3b064408d0cfdda9a3538887188'], + # }), + # ('IO::Handle', '1.42', { + # 'source_tmpl': 'IO-%(version)s.tar.gz', + # 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + # 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], + # }), + # ('Test::More', '1.302171', { + # 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + # 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + # 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], + # }), ('Bio::ASN1::EntrezGene', '1.73', { - 'source_tmpl': 'Bio-ASN1-EntrezGene-1.73.tar.gz', + 'source_tmpl': 'Bio-ASN1-EntrezGene-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], 'checksums': ['f9e778db705ce5c35ad2798e38a8490b644edfdc14253aa1b74a1f5e79fc6a4b'], }), - ('Cwd', '3.75', { - 'source_tmpl': 'PathTools-3.75.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], - }), - ('Data::Dumper', '2.173', { - 'source_tmpl': 'Data-Dumper-2.173.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], - }), - ('LWP::UserAgent', '6.06', { - 'source_tmpl': 'libwww-perl-6.43.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], - }), + # ('Cwd', '3.75', { + # 'source_tmpl': 'PathTools-%(version)s.tar.gz', + # 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + # 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + # }), + # ('Data::Dumper', '2.173', { + # 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + # 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + # 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + # }), + # ('LWP::UserAgent', '6.43', { + # 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + # 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + # 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], + # }), ('Text::Wrap', '2013.0523', { - 'source_tmpl': 'Text-Tabs+Wrap-2013.0523.tar.gz', + 'source_tmpl': 'Text-Tabs+Wrap-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MU/MUIR/modules'], 'checksums': ['b9cb056fffb737b9c12862099b952bf4ab4b1f599fd34935356ae57dab6f655f'], }), ('base', '2.23', { - 'source_tmpl': 'base-2.23.tar.gz', + 'source_tmpl': 'base-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['40f55841299a9fe6fab03cd098f94e9221fb516978e9ef40fd8ff2cbd6625dde'], }), @@ -74,7 +74,7 @@ exts_list = [ ] # Need to run tests after install to get perl modules on perl path. -sanity_check_commands = ["cd %(builddir)s/BioDBEUtilities/Bio-EUtilities-1.76 && make test"] +sanity_check_commands = ["cd %(builddir)s/BioDBEUtilities/Bio-EUtilities-%(version)s && make test"] modextrapaths = { 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', diff --git a/easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb deleted file mode 100644 index c9d5062e915..00000000000 --- a/easybuild/easyconfigs/l/LWP-Protocol-https/LWP-Protocol-https-6.07-GCCcore-8.3.0.eb +++ /dev/null @@ -1,72 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'Bundle' - -name = 'LWP-Protocol-https' -version = '6.07' - -homepage = 'https://github.com/libwww-perl/lwp-protocol-https' -description = "Provide https support for LWP::UserAgent" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -builddependencies = [('binutils', '2.32')] -dependencies = [ - ('Perl', '5.30.0'), -] - -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('LWP::UserAgent', '6.06', { - 'source_tmpl': 'libwww-perl-6.43.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], - }), - ('Mozilla::CA', '20110101', { - 'source_tmpl': 'Mozilla-CA-20180117.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], - 'checksums': ['f2cc9fbe119f756313f321e0d9f1fac0859f8f154ac9d75b1a264c1afdf4e406'], - }), - ('Net::HTTPS', '6', { - 'source_tmpl': 'Net-HTTP-6.19.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['52b76ec13959522cae64d965f15da3d99dcb445eddd85d2ce4e4f4df385b2fc4'], - }), - ('Net::HTTPS', '6', { - 'source_tmpl': 'Net-HTTP-6.19.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['52b76ec13959522cae64d965f15da3d99dcb445eddd85d2ce4e4f4df385b2fc4'], - }), - ('Test::More', '0', { - 'source_tmpl': 'Test-Simple-1.302171.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], - }), - ('Test::RequiresInternet', '0', { - 'source_tmpl': 'Test-RequiresInternet-0.05.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN/'], - 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], - }), - ('LWP::Protocol::https', version, { - 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['522cc946cf84a1776304a5737a54b8822ec9e79b264d0ba0722a70473dbfb9e7'], - }), -] - -# Need to run tests after install to get perl modules on perl path. -sanity_check_commands = ["cd %(builddir)s/LWPProtocolhttps/LWP-Protocol-https-6.07 && make test"] - -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb index 0fef1d578f4..f79876cb5ce 100644 --- a/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb @@ -1,7 +1,7 @@ # Author: Pavel Grochal (INUITS) # License: GPLv2 -easyblock = 'Bundle' +easyblock = 'PerlModule' name = 'swissknife' version = '1.79' @@ -11,33 +11,19 @@ description = "Perl module for reading and writing UniProtKB data in plain text toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +source_urls = [('https://sourceforge.net/projects/swissknife/files/swissknife/1.79', 'download')] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['a7affa6ed892a8d9f4f9f1297d521076ac5bb1adfd85de5dc041679b53b949d6'] + + builddependencies = [('binutils', '2.32')] dependencies = [ ('Perl', '5.30.0'), ] -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('Data::Dumper', '2.173', { - 'source_tmpl': 'Data-Dumper-2.173.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], - }), - ('SWISS::Entry', version, { - 'source_tmpl': 'swissknife_%(version)s.tar.gz', - 'source_urls': [('https://sourceforge.net/projects/swissknife/files/swissknife/1.79', 'download')], - 'checksums': ['a7affa6ed892a8d9f4f9f1297d521076ac5bb1adfd85de5dc041679b53b949d6'], - }), -] +runtest = "test TEST_VERBOSE=1" -# Need to run tests after install to get perl modules on perl path. -sanity_check_commands = ["cd %(builddir)s/SWISSEntry/swissknife_1.79 && make test"] - -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} +options = {'modulename': 'SWISS::Entry'} sanity_check_paths = { 'files': [], From 10bbabb259533f4c09c1a2f52d8ea2c8a822ee1f Mon Sep 17 00:00:00 2001 From: build Date: Thu, 16 Apr 2020 14:18:13 +0200 Subject: [PATCH 105/431] adding easyconfigs: gretl-2020a-foss-2019a.eb --- .../g/gretl/gretl-2020a-foss-2019a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb diff --git a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb new file mode 100644 index 00000000000..c7a88b3cb1d --- /dev/null +++ b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Loris Bennett +# ZEDAT, Freie Universitaet Berlin + +easyblock = 'ConfigureMake' + +name = 'gretl' +version = '2020a' + +homepage = 'http://gretl.sourceforge.net' +description = "A cross-platform software package for econometric analysis" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'openmp': True} + +#http://prdownloads.sourceforge.net/gretl/gretl-2020a.tar.xz +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['4c369f33c9aa825920229263bfd12560168c4e46282240bee3497436a7ae9b7b'] + +builddependencies = [ + ('gnuplot', '5.2.6'), + ('libxml2', '2.9.8'), + ('GMP', '6.1.2'), + ('GtkSourceView', '3.24.11'), + ('ImageMagick', '7.0.8-46'), + ('MPFR', '4.0.2'), +] + + +preconfigopts = 'export LDFLAGS="-fopenmp $LDFLAGS" && ' + +configopts = '--disable-json ' + +sanity_check_paths = { + 'files': ['bin/gretl', 'bin/gretlcli'], + 'dirs': ['bin', 'share'] +} + +moduleclass = 'math' From e216d06f4a83056691cb70afe4603aea7ea062a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 14:52:00 +0200 Subject: [PATCH 106/431] add patch for AutoMap to avoid that it to create a log file in installation directory --- .../a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb | 6 +++++- .../AutoMap-1.0-foss-2019b-20200324_fix-log.patch | 14 ++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324_fix-log.patch diff --git a/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb index 0acf9d32ad4..4a177e8b67f 100644 --- a/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb +++ b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb @@ -15,7 +15,11 @@ sources = [{ 'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ, }] -checksums = ['cbf60a89984ee0e0119e362be5b620c1f28182d765280bd08c0ba6f9c7697625'] +patches = ['AutoMap-%(version)s-foss-2019b%(versionsuffix)s_fix-log.patch'] +checksums = [ + 'cbf60a89984ee0e0119e362be5b620c1f28182d765280bd08c0ba6f9c7697625', # AutoMap-1.0.tar.gz + 'a381f130217b92a7c961234e8255c96c9ff76e2a002277c23b99f14dcacb17c6', # AutoMap-1.0-foss-2019b-20200324_fix-log.patch +] dependencies = [ ('BCFtools', '1.10.2'), diff --git a/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324_fix-log.patch b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324_fix-log.patch new file mode 100644 index 00000000000..9a9a702c39e --- /dev/null +++ b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324_fix-log.patch @@ -0,0 +1,14 @@ +avoid that AutoMap tries to create a log file in installation directory, +log to current directory instead using PID of current process +author: Kenneth Hoste (HPC-UGent) +--- AutoMap_v1.0.sh.orig 2020-04-16 14:34:15.327400539 +0200 ++++ AutoMap_v1.0.sh 2020-04-16 14:33:57.979381000 +0200 +@@ -241,7 +241,7 @@ + vcf=${vcfs[$k]} + id=${ids[$k]} + +- here="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )" ++ here="$PWD/AutoMap_pid$$" + + nbvar=$(grep -v "#" $vcf | grep -P "AD|DP4" | grep GT | wc -l) + From c6a77eae6e282d2193f676b7bc00af47aa10d2d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 14:52:36 +0200 Subject: [PATCH 107/431] adding easyconfigs: StringTie-2.1.1-GCC-8.3.0.eb --- .../s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb new file mode 100644 index 00000000000..25e7f19a7e6 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.1.1' + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea152b791856b1bd5dd2d475b06fae05398ee7e03f2f9844418010376edcca2'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +# the test script downloads some test data from the internet +buildopts = 'release && ./run_tests.sh' + +files_to_copy = [ + (['stringtie', 'prepDE.py'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/stringtie'], + 'dirs': [], +} + +moduleclass = 'bio' From 9cb39db900f9160b2bcbd9d809fb02719c799519 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 15:05:14 +0200 Subject: [PATCH 108/431] add missin binutils build dep in StringTie 2.1.1 easyconfig --- easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb index 25e7f19a7e6..08cb149dc6e 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.1.1-GCC-8.3.0.eb @@ -17,6 +17,7 @@ source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7ea152b791856b1bd5dd2d475b06fae05398ee7e03f2f9844418010376edcca2'] +builddependencies = [('binutils', '2.32')] dependencies = [ ('zlib', '1.2.11'), ] From 7a16d59d7c81e866490affcb48285f181a6f2ca3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 16:08:19 +0200 Subject: [PATCH 109/431] add Perl build dep to Autoconf/Automake easyconfigs using GCCcore/9.3.0 toolchain --- .../easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb | 3 +++ .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb index 1e2780e6f96..421245c596f 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-9.3.0.eb @@ -22,6 +22,9 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] builddependencies = [ ('binutils', '2.34'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.30.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb index 89abe4f1110..00bb8cb6910 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-9.3.0.eb @@ -27,6 +27,9 @@ checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] builddependencies = [ ('binutils', '2.34'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.30.2'), ] dependencies = [ From c545bae4d4193ae52d6d4c0843c2a5732d061bd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 16:15:57 +0200 Subject: [PATCH 110/431] adding easyconfigs: Racon-1.4.13-GCCcore-8.3.0.eb --- .../r/Racon/Racon-1.4.13-GCCcore-8.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..875c13c3311 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.4.13' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4220e98bf84768483bd94eef62a0821cffc74f4e7139c74685c08161909263b0'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From bfa256261e6f2e0708aa0c445bdf1b8575bee65f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 16 Apr 2020 17:30:02 +0200 Subject: [PATCH 111/431] Update ICU-64.2-GCCcore-8.3.0.eb fix download link --- easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb index 063a8445d12..926cfcd62e0 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.3.0.eb @@ -10,7 +10,7 @@ description = """ICU is a mature, widely used set of C/C++ and Java libraries pr toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] From e513938f597940a79d72b1a9746b173c75bdb3e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 17:55:18 +0200 Subject: [PATCH 112/431] disable USER-INTEL package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results --- .../LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 6 +++++- .../LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 797c61b5d49..97bd1f7b628 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,11 @@ dependencies = [ # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. # https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options -# configopts = " " + +# having the USER-INTEL package (https://lammps.sandia.gov/doc/Speed_intel.html) enabled with intel/2019b +# results in a LAMMPS installation that yields incorrect results, +# so disable this particular package for now... +configopts = '-DPKG_USER-INTEL=off' # auto-enabled by easyblock # 'GPU' - if cuda package is present and kokkos is disabled diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index 99dde72b8fe..4f70c0fcd7d 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,11 @@ dependencies = [ # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. # https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options -# configopts = " " + +# having the USER-INTEL package (https://lammps.sandia.gov/doc/Speed_intel.html) enabled with intel/2019b +# results in a LAMMPS installation that yields incorrect results, +# so disable this particular package for now... +configopts = '-DPKG_USER-INTEL=off' # auto-enabled by easyblock # 'GPU' - if cuda package is present and kokkos is disabled From 3f2aae0ca3181a150282cfda159fa0bf5fc37c8e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Apr 2020 18:05:51 +0200 Subject: [PATCH 113/431] AutoMap v1.0: remove patch leftovers --- .../easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb index 4a177e8b67f..bcdd449eb7f 100644 --- a/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb +++ b/easybuild/easyconfigs/a/AutoMap/AutoMap-1.0-foss-2019b-20200324.eb @@ -30,7 +30,10 @@ dependencies = [ fix_perl_shebang_for = ['Scripts/*.pl'] -postinstallcmds = ["chmod a+x %(installdir)s/AutoMap_v%(version)s.sh"] +postinstallcmds = [ + "chmod a+x %(installdir)s/AutoMap_v%(version)s.sh", + "rm %(installdir)s/AutoMap_v%(version)s.sh.orig", # remove leftovers from patch +] sanity_check_paths = { 'files': ['AutoMap_v%(version)s.sh'], From 5fa13ebddd1eae37fa5086c63626bf51769b32ca Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 16 Apr 2020 17:49:42 +0000 Subject: [PATCH 114/431] Add {bio}[foss/2019a] FSL v6.0.2 w/ Python 2.7.15 --- .../FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..0b47d8a4ab2 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,79 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Some tools like icmp are missing since they are built with the fslpython_install.sh script +# which locally installs Miniconda and creates a virtual environment. This is too messy and +# an alternative solution is necessary to install them. +# https://github.com/easybuilders/easybuild-easyconfigs/issues/7899 +# https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation#imcp.2Fimglob.2Fimmv_errors_after_installation + +name = 'FSL' +version = '6.0.2' +versionsuffix = '-Python-2.7.15' + +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ["https://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.2_Makefile_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + 'c118b351c6cedb441af7e1b9d194cf344505ff53b417063f697b86305a908afd', # fsl-6.0.2-sources.tar.gz + '4212478ef24be4bce7a9ce513aa9c45fcf67eccfe064331a2e8e52be41d3513c', # FSL-6.0.2_Makefile_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +dependencies = [ + ('Boost', '1.70.0'), + ('libgd', '2.2.5'), + ('libxml2', '2.9.8'), + ('libxml++', '2.40.1'), + ('SQLite', '3.27.2'), + ('libpng', '1.6.36'), + ('Tk', '8.6.9'), + ('NLopt', '2.6.1'), + ('freeglut', '3.0.0'), + ('expat', '2.2.6'), + ('zlib', '1.2.11'), + ('VTK', '8.2.0', versionsuffix), + ('GSL', '2.5'), + ('Qwt', '6.1.4'), +] + +# FSLDIR needs to be defined when running postinstall to get the correct shebang +# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1910&L=FSL&P=R86209 +postinstallcmds = [( + 'FSLDIR=%(installdir)s PATH=%(installdir)s/fsl/fslpython/bin:$PATH ' + '%(installdir)s/fsl/etc/fslconf/post_install.sh -f %(installdir)s/fsl; ' +)] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +# +# Adding the bin from the virtualenv was the only way to get things working... +# +# NOTE: This did after extensiv tests not apply to the 2019a toolchain, please see +# https://github.com/easybuilders/easybuild-easyconfigs/issues/9654 +# +# modextrapaths = { +# 'PATH': 'fsl/fslpython/bin', +# 'PYTHONPATH': 'fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/', +# } + +moduleclass = 'bio' From 375561df4a1fbfa7afdb133823d66d3e12d86607 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 16 Apr 2020 21:04:06 +0200 Subject: [PATCH 115/431] adding easyconfigs: GlobalArrays-5.7.2-intel-2019a.eb, GlobalArrays-5.7.2-intel-2019a-peigs.eb --- .../GlobalArrays-5.7.2-intel-2019a-peigs.eb | 33 +++++++++++++++++++ .../GlobalArrays-5.7.2-intel-2019a.eb | 27 +++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb new file mode 100644 index 00000000000..5a144e41ccb --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb @@ -0,0 +1,33 @@ +# Includes the parallel eigen value solver (used by NWChem). +# This requires additional external symbols during linking, so it won't work for software that doesn't use it. + +easyblock = 'ConfigureMake' +name = 'GlobalArrays' +version = '5.7.2' +versionsuffix = '-peigs' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['8cd0fcfd85bc7f9c168c831616f66f1e8b9b2ca31dc7dd93cc55b27cc7fe7069'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' +# Required by NWChem: +configopts += ' --enable-peigs --enable-underscoring' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb new file mode 100644 index 00000000000..a404cc5a4bc --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' +name = 'GlobalArrays' +version = '5.7.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['8cd0fcfd85bc7f9c168c831616f66f1e8b9b2ca31dc7dd93cc55b27cc7fe7069'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 6e8b62648135f3f9cb87bc86a0d28d68188a41fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Apr 2020 21:27:59 +0200 Subject: [PATCH 116/431] FusionCatcher-1.20: add comments about use of BLAT and Kent_tools --- .../FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb index 328e19e1981..60de7990626 100644 --- a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb @@ -17,17 +17,17 @@ dependencies = [ ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), ('Biopython', '1.75', versionsuffix), - ('BLAT', '3.5'), + ('BLAT', '3.5'), # preferred over Kent_tools as BLAT is built from source ('Bowtie', '1.2.3'), ('Bowtie2', '2.3.5.1'), ('BWA', '0.7.17'), - ('Kent_tools', '20190326', '-linux.x86_64', True), + ('Kent_tools', '20190326', '-linux.x86_64', True), # only used for liftover ('SRA-Toolkit', '2.10.4'), ('STAR', '2.7.2b'), - ('picard', '2.21.6', '-Java-11', True), # Optional - ('Velvet', '1.2.10', '-mt-kmer_191'), # Optional - ('OpenPyXL', '2.6.4'), # Optional - ('parallel', '20190922'), # Optional + ('picard', '2.21.6', '-Java-11', True), # optional + ('Velvet', '1.2.10', '-mt-kmer_191'), # optional + ('OpenPyXL', '2.6.4'), # optional + ('parallel', '20190922'), # optional ('pigz', '2.4'), ('zlib', '1.2.11'), ] From 6e181ec15dcb5ab02a831726b96413a526b19c24 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 17 Apr 2020 05:44:24 +1000 Subject: [PATCH 117/431] Update and rename zsh-5.8-foss-2019b.eb to zsh-5.8-GCC-8.3.0.eb --- .../z/zsh/{zsh-5.8-foss-2019b.eb => zsh-5.8-GCC-8.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/z/zsh/{zsh-5.8-foss-2019b.eb => zsh-5.8-GCC-8.3.0.eb} (84%) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.8-GCC-8.3.0.eb similarity index 84% rename from easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb rename to easybuild/easyconfigs/z/zsh/zsh-5.8-GCC-8.3.0.eb index babb3ea8fe8..12988c1db9c 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.8-foss-2019b.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.8-GCC-8.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'zsh' version = '5.8' -homepage = 'http://www.zsh.org/' +homepage = 'https://www.zsh.org/' description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." toolchain = {'name': 'GCC', 'version': '8.3.0'} sources = [SOURCELOWER_TAR_XZ] -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +source_urls = ['https://prdownloads.sourceforge.net/%(namelower)s'] checksums = ['dcc4b54cc5565670a65581760261c163d720991f0d06486da61f8d839b52de27'] dependencies = [ From 448c2b662458a79157735ee98e9f5d6bcf784833 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 16 Apr 2020 23:59:29 -0500 Subject: [PATCH 118/431] Two new ROOT-based Python numeric modules, for use with HEP analysis code. --- ...oot_numpy-4.8.0-foss-2018b-Python-3.6.6.eb | 40 +++++++++++++++++++ .../rootpy-1.0.1-foss-2018b-Python-3.6.6.eb | 38 ++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..f2c2fb59b3b --- /dev/null +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Texas A&M University, Mitchell Institute for +# Fundamental Physics and Astronomy +# +# Homepage:: http://mitchell.tamu.edu/ +# +# Copyright:: Copyright 2020 Texas A&M University +# Author:: Michael Kelsey +# License:: CC BY-SA 4.0 +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'root_numpy' +version = '4.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-hep.org/root_numpy/' +description = """root_numpy is a Python extension module that provides +an efficient interface between ROOT and NumPy. root_numpy’s internals +are compiled C++ and can therefore handle large amounts of data much +faster than equivalent pure Python implementations.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '5842bbcde92133f60a61f56e9f0a875a0dbc2a567cc65a9ac141ecd72e416878', # root_numpy-4.8.0.zip +] + +dependencies = [ + ('Python', '3.6.6'), + ('ROOT', '6.14.06', versionsuffix), + ('numpy', '1.18.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..39fbf6998fd --- /dev/null +++ b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'rootpy' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.rootpy.org/' + +description = """The rootpy project is a community-driven initiative aiming to +provide a more pythonic interface with ROOT on top of the existing +PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy +also aims to improve ROOT design flaws and supplement existing ROOT +functionality. The scientific Python community also offers a multitude +of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, +and PyTables, but a suitable interface between them and ROOT has been +lacking. rootpy provides the interfaces and conversion mechanisms +required to liberate your data and to take advantage of these +alternatives if needed.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7d85fc8fc4ff96a833fa593be401aa4836b755757b518d23d4c00d7a105ce27e'] + +dependencies = [ + ('Python', '3.6.6'), + ('ROOT', '6.14.06', versionsuffix), + ('matplotlib', '3.0.0', versionsuffix), + ('PyTables', '3.4.4', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' From 182f4e384fca012a70fc5931d607d015ce281f3f Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 17 Apr 2020 10:02:50 +0200 Subject: [PATCH 119/431] Updated ray, included separate protobuf --- ...f-python-3.10.0-foss-2019b-Python-3.7.4.eb | 30 +++++++++++++++++++ .../Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb | 16 ++++------ 2 files changed, 36 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..62fc89ee0b2 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/google/protobuf/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['83a3a0b23ed2b08041dbb0af92d023e5325a4324c2bc8acb55962d349710e52f'] + +dependencies = [ + ('Python', '3.7.4'), + ('protobuf', version) +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb index f1be3a65860..f5da9ef70cf 100644 --- a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb @@ -5,19 +5,19 @@ easyblock = 'PythonBundle' name = 'Ray' version = '0.8.4' + versionsuffix = '-Python-%(pyver)s' homepage = "https://docs.ray.io/en/latest/" description = "Ray is a fast and simple framework for building and running distributed applications." toolchain = {'name': 'foss', 'version': '2019b'} - -builddependencies = [('pkg-config', '0.29.2')] +toolchainopts = {'usempi': True} dependencies = [ ('Python', '3.7.4'), - ('Bazel', '0.29.1'), ('SciPy-bundle', '2019.10', versionsuffix), + ('protobuf-python', '3.10.0', versionsuffix), ] use_pip = True @@ -86,10 +86,6 @@ exts_list = [ ('msgpack', '1.0.0', { 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], }), - ('protobuf', '3.11.3', { - 'modulename': 'google.protobuf', - 'checksums': ['c77c974d1dadf246d789f6dad1c24426137c9091e930dbf50e0a29c1fcf00b1f'], - }), ('py-spy', '0.3.3', { 'modulename': False, 'source_tmpl': 'py_spy-%(version)s-py2.py3-none-manylinux1_x86_64.whl', @@ -103,17 +99,17 @@ exts_list = [ ('redis', '3.4.1', { 'checksums': ['0dcfb335921b88a850d461dc255ff4708294943322bd55de6cfd68972490ca1f'], }), + # Ray is run from wheel, because build doesn't pass LD_LIBRARY_PATH properly to Bazel/Protobuf + # https://github.com/ray-project/ray/issues/5274 (name, version, { 'source_tmpl': '%(namelower)s-%(version)s-cp37-cp37m-manylinux1_x86_64.whl', 'unpack_sources': False, 'checksums': ['f2cca186a9f8a18f9d58eadcd8ea126addc3192e922f36a7ced46b8b8904ac65'], }), - ] -local_bin_files = ['google', 'jsonschema', 'py-spy', 'ray', 'rllib', 'tune'] sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], + 'files': ['bin/ray'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ From c927830b7aceb5203e48d91e87947124c30da44d Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 17 Apr 2020 10:06:14 +0200 Subject: [PATCH 120/431] moved pyyaml to deps --- .../easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb index f5da9ef70cf..d2f1e472dfd 100644 --- a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb @@ -18,6 +18,7 @@ dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('protobuf-python', '3.10.0', versionsuffix), + ('PyYAML', '5.1.2'), ] use_pip = True @@ -92,10 +93,6 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['e9d6946741c267fe82aef18d2fc1e095a90a83fb5f3d9fc89b0f20a39613a639'], }), - ('PyYAML', '5.3.1', { - 'modulename': 'yaml', - 'checksums': ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'], - }), ('redis', '3.4.1', { 'checksums': ['0dcfb335921b88a850d461dc255ff4708294943322bd55de6cfd68972490ca1f'], }), From b631fdb2b5c19c1360d92d4163a6e55eaba0637f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 10:38:57 +0200 Subject: [PATCH 121/431] add short test case for LAMMPS in sanity check to catch problems caused by USER-INTEL package --- ...3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb | 14 +- ...Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 14 +- ...7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb | 14 +- ...Aug2019-intel-2019b-Python-3.7.4-kokkos.eb | 14 +- ...lammps_vs_yaff_test_single_point_energy.py | 1325 +++++++++++++++++ 5 files changed, 1373 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/l/LAMMPS/lammps_vs_yaff_test_single_point_energy.py diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index 2203d1a7153..92d59f7fb16 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -21,8 +21,14 @@ toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1'] +sources = [ + 'stable_%(version)s.tar.gz', + {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz + '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py +] local_source_dir_name = '%(namelower)s-%(version)s' @@ -85,4 +91,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +# run short test case to make sure installation doesn't produce blatently incorrect results; +# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b +sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 97bd1f7b628..5db45529939 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -21,8 +21,14 @@ toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1'] +sources = [ + 'stable_%(version)s.tar.gz', + {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz + '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py +] local_source_dir_name = '%(namelower)s-%(version)s' @@ -89,4 +95,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +# run short test case to make sure installation doesn't produce blatently incorrect results; +# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b +sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index 404a6a345aa..9deb6f6138b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -21,8 +21,14 @@ toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f'] +sources = [ + 'stable_%(version)s.tar.gz', + {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz + '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py +] local_source_dir_name = '%(namelower)s-%(version)s' @@ -85,4 +91,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +# run short test case to make sure installation doesn't produce blatently incorrect results; +# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b +sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index 4f70c0fcd7d..74be8e3fe61 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -21,8 +21,14 @@ toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f'] +sources = [ + 'stable_%(version)s.tar.gz', + {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz + '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py +] local_source_dir_name = '%(namelower)s-%(version)s' @@ -89,4 +95,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +# run short test case to make sure installation doesn't produce blatently incorrect results; +# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b +sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/lammps_vs_yaff_test_single_point_energy.py b/easybuild/easyconfigs/l/LAMMPS/lammps_vs_yaff_test_single_point_energy.py new file mode 100644 index 00000000000..7827c7b7704 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/lammps_vs_yaff_test_single_point_energy.py @@ -0,0 +1,1325 @@ +#!/usr/bin/env python +# +# Correctness test for LAMMPS, comparison with result produced by yaff; +# calculates single-point energy with both LAMMPS and yaff, and compares the results. +# The energy difference should not exceed 1 kJ/mol, otherwise an error is raised. +# It should run to completion in a matter of seconds. +# +# If this test passes, there are no guarantees that the installation works fully correctly. +# But if it fails, it's a strong signal that there is something wrong with the (LAMMPS) installation. +# +# author: Veronique Van Speybroeck (Center for Molecular Modeling, Ghent University), April 2020 + +import numpy as np +import os +import h5py +from mpi4py import MPI +from glob import glob +from yaff import * +from molmod import kjmol +from io import StringIO +import tempfile + + +def main(): + + # create input files in temporary directory + tmpdir = tempfile.mkdtemp() + + init_chk = os.path.join(tmpdir, 'init.chk') + with open(init_chk, 'w') as fp: + fp.write(INIT_CHK) + + pars_txt = os.path.join(tmpdir, 'pars.txt') + with open(pars_txt, 'w') as fp: + fp.write(PARS_TXT) + + # Setup MPI + comm = MPI.COMM_WORLD + rank = comm.Get_rank() + + # Set random seed, important to get the same velocities for all processes + np.random.seed(5) + # Turn off logging for all processes, it can be turned on for one selected process later on + log.set_level(log.silent) + if rank==0: log.set_level(log.medium) + + # Load in the structure and the force field + system = System.from_file(init_chk) + + # Initialize the Yaff and LAMMPS force fields + rcut = 12*angstrom + ff_yaff = ForceField.generate(system, pars_txt, rcut=rcut, smooth_ei=False, gcut_scale=1.5, alpha_scale=3.2)#, tailcorrections=True) + ff = swap_noncovalent_lammps(ff_yaff, fn_system='lammps.dat', fn_log="log.lammps", suffix='', fn_table='lammps_smoothei2.table', comm=comm) + + # Print out the Yaff single-point energy + print('Yaff energy') + energy_yaff = ff_yaff.compute() + print(energy_yaff/kjmol) + for part in ff_yaff.parts: + print('%s: %.3f kJ/mol' %(part.name,part.energy/kjmol)) + + # Print out the LAMMPS single-point energy + print('LAMMPS energy') + energy_lammps = ff.compute() + print(energy_lammps/kjmol) + for part in ff.parts: + print('%s: %.3f kJ/mol' %(part.name,part.energy/kjmol)) + + assert np.abs(energy_yaff- energy_lammps) < 1*kjmol, "The two energies are not the same" + + +INIT_CHK = """bonds kind=intar 592,2 + 52 14 74 14 + 130 14 4 52 + 4 92 112 4 + 152 71 152 112 + 176 74 176 127 + 92 180 130 180 + 200 176 224 180 + 152 228 52 348 + 11 52 11 71 + 11 127 53 15 + 75 15 131 15 + 53 5 93 5 + 113 5 153 70 + 153 113 177 75 + 177 126 181 93 + 131 181 201 177 + 225 181 153 229 + 349 53 10 53 + 10 70 10 126 + 12 54 72 12 + 128 12 6 54 + 6 94 114 6 + 154 69 154 114 + 72 178 178 125 + 94 182 128 182 + 202 178 226 182 + 154 230 54 350 + 9 54 9 69 + 9 125 8 41 + 56 8 8 148 + 56 165 107 165 + 173 103 145 173 + 185 97 185 148 + 185 213 221 165 + 233 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1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 + 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 1.368161720958986e+00 +radii2 kind=none None +rvecs kind=fltar 3,3 + 3.979364985026868e+01 7.614451550399652e-06 -6.349718219381480e-06 7.617082337342254e-06 + 3.979363720174106e+01 1.466093923475890e-05 -6.348208809181665e-06 1.466769197263813e-05 + 3.979365172754711e+01 +scope_ids kind=none None +scopes kind=none None +valence_charges kind=none None +""" + +PARS_TXT = """# BONDHARM +#--------- +BONDHARM:UNIT K kjmol/A**2 +BONDHARM:UNIT R0 A + +BONDHARM:PARS O_OH ZR 3.7856874859e+02 2.2345796544e+00 +BONDHARM:PARS O_CA ZR 8.4085734618e+02 2.1879092596e+00 +BONDHARM:PARS O_OX ZR 7.5654881429e+02 2.1161540051e+00 +BONDHARM:PARS C_CA O_CA 4.4101463252e+03 1.2792436607e+00 +BONDHARM:PARS C_CA C_PC 2.1038566297e+03 1.4832348712e+00 +BONDHARM:PARS C_PC C_PH 3.2247609625e+03 1.4015678878e+00 +BONDHARM:PARS C_PH C_PH 3.3880065753e+03 1.3929483296e+00 +BONDHARM:PARS C_PH H_PH 3.3762726364e+03 1.0876572905e+00 +BONDHARM:PARS H_OH O_OH 5.0216717525e+03 9.9986798534e-01 + + +# BENDAHARM +#---------- +BENDAHARM:UNIT K kjmol/rad**2 +BENDAHARM:UNIT THETA0 deg + +BENDAHARM:PARS ZR O_OH ZR 4.1362556428e+02 1.0775418131e+02 +BENDAHARM:PARS C_CA O_CA ZR 2.6430192082e+02 1.3689725294e+02 +BENDAHARM:PARS C_PH C_PH H_PH 3.0835003755e+02 1.2017556632e+02 +BENDAHARM:PARS C_PC C_CA O_CA 1.6684448679e+02 1.1975013868e+02 +BENDAHARM:PARS C_CA C_PC C_PH 6.0256074066e+02 1.1990380480e+02 +BENDAHARM:PARS C_PC C_PH C_PH 4.7103023496e+02 1.2003765295e+02 +BENDAHARM:PARS O_CA C_CA O_CA 6.8388715389e+02 1.2311437675e+02 +BENDAHARM:PARS O_OH ZR O_OX 5.3052365716e+02 6.4534430940e+01 +BENDAHARM:PARS C_PH C_PC C_PH 4.2496973028e+02 1.1972403242e+02 +BENDAHARM:PARS C_PC C_PH H_PH 2.9895866247e+02 1.1956474865e+02 +BENDAHARM:PARS ZR O_OX ZR 5.0533812788e+02 1.2046678892e+02 +BENDAHARM:PARS H_OH O_OH ZR 1.7902855792e+02 1.1039262816e+02 +BENDAHARM:PARS O_OX ZR O_OX 1.0039193248e+02 6.3800382263e+01 + + +# TORSION +#-------- +TORSION:UNIT A kjmol +TORSION:UNIT PHI0 deg + +TORSION:PARS C_PH C_PC C_PH C_PH 2 3.4910522540e+01 0.0000000000e+00 +TORSION:PARS O_CA C_CA O_CA ZR 2 7.0218267368e+00 0.0000000000e+00 +TORSION:PARS C_CA C_PC C_PH C_PH 2 4.6013908971e+01 0.0000000000e+00 +TORSION:PARS C_PH C_PC C_PH H_PH 2 2.8550678889e+01 0.0000000000e+00 +TORSION:PARS C_CA C_PC C_PH H_PH 2 1.8865768343e+01 0.0000000000e+00 +TORSION:PARS C_PC C_CA O_CA ZR 2 3.2834550916e+01 0.0000000000e+00 +TORSION:PARS C_PC C_PH C_PH H_PH 2 3.3870440544e+01 0.0000000000e+00 +TORSION:PARS H_PH C_PH C_PH H_PH 2 1.7461761843e+01 0.0000000000e+00 +TORSION:PARS C_PH C_PC C_CA O_CA 2 1.3072558996e+01 0.0000000000e+00 + + +# OOPDIST +#-------- +OOPDIST:UNIT K kjmol/A**2 +OOPDIST:UNIT D0 A + +OOPDIST:PARS C_PC O_CA O_CA C_CA 1.3685283732e+03 0.0000000000e+00 +OOPDIST:PARS C_PC C_PH H_PH C_PH 2.0695840516e+02 0.0000000000e+00 + + +#Fixed charges +#--------------- + +FIXQ:UNIT Q0 e +FIXQ:UNIT P e +FIXQ:UNIT R angstrom +FIXQ:SCALE 1 1.0 +FIXQ:SCALE 2 1.0 +FIXQ:SCALE 3 1.0 +FIXQ:DIELECTRIC 1.0 + +# Atomic parameters +# ---------------------------------------------------- +# KEY label Q_0A R_A +# ---------------------------------------------------- +FIXQ:ATOM ZR 0.0000000000000 2.3670000000 +FIXQ:ATOM CE 0.0000000000000 2.3670000000 +FIXQ:ATOM O_OH 0.0000000000000 1.1180000000 +FIXQ:ATOM O_OX 0.0000000000000 1.1180000000 +FIXQ:ATOM O_CA 0.0000000000000 1.1180000000 +FIXQ:ATOM C_PH 0.0000000000000 1.1630000000 +FIXQ:ATOM C_PC 0.0000000000000 1.1630000000 +FIXQ:ATOM C_CA 0.0000000000000 1.1630000000 +FIXQ:ATOM H_PH 0.0000000000000 0.7240000000 +FIXQ:ATOM H_OH 0.0000000000000 0.7240000000 + +# Bond parameters +# ---------------------------------------------------- +# KEY label0 label1 P_AB +# ---------------------------------------------------- +FIXQ:BOND C_PH C_PH 0.0000928607 +FIXQ:BOND C_CA C_PC 0.0432515406 +FIXQ:BOND O_CA ZR -0.3140076067 +FIXQ:BOND O_OX ZR -0.3646234389 +FIXQ:BOND C_PH H_PH -0.1385876479 +FIXQ:BOND H_OH O_OH 0.4906092530 +FIXQ:BOND C_CA O_CA 0.3691317391 +FIXQ:BOND C_PC C_PH -0.0556062459 +FIXQ:BOND O_OH ZR -0.1881444503 + +# van der Waals +#============== + +# The following mathemetical form is supported: +# - MM3: EPSILON*(1.84e5*exp(-12*r/SIGMA)-2.25*(SIGMA/r)^6) +# - LJ: 4.0*EPSILON*((SIGMA/r)^12 - (SIGMA/r)^6) +# +# Remark: +# In MM3, if ONLYPAULI=1 then only the pauli term will be used. +# If ONLYPAULI=0, the full MM3 expression is used with 12. + +MM3:UNIT SIGMA angstrom +MM3:UNIT EPSILON kcalmol +MM3:SCALE 1 0.0 +MM3:SCALE 2 0.0 +MM3:SCALE 3 1.0 + +# --------------------------------------------- +# KEY ffatype SIGMA EPSILON ONLYPAULI +# --------------------------------------------- +MM3:PARS ZR 2.540 0.300 0 +MM3:PARS CE 2.740 0.340 0 +MM3:PARS HF 2.530 0.516 0 +MM3:PARS O_CA 1.820 0.059 0 +MM3:PARS O_OX 1.820 0.059 0 +MM3:PARS O_OH 1.820 0.059 0 +MM3:PARS C_CA 1.940 0.056 0 +MM3:PARS C_PC 1.960 0.056 0 +MM3:PARS C_PH 1.960 0.056 0 +MM3:PARS H_OH 1.600 0.016 0 +MM3:PARS H_PH 1.620 0.020 0 +MM3:PARS C_FO 1.940 0.056 0 +MM3:PARS H_FO 1.620 0.020 0 +""" + + +main() From 5e3b93cffd32e4bb5b3f91f77f85569896f6b69d Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 17 Apr 2020 10:40:13 +0200 Subject: [PATCH 122/431] moved some extensions to deps --- .../augur-7.0.2-intel-2019b-Python-3.7.4.eb | 29 ++++--------------- 1 file changed, 5 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb index 07266e3d30f..30d6c3f6037 100644 --- a/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/augur/augur-7.0.2-intel-2019b-Python-3.7.4.eb @@ -23,6 +23,9 @@ dependencies = [ ('FastTree', '2.1.11'), ('CVXOPT', '1.2.4', versionsuffix), ('matplotlib', '3.1.1', versionsuffix), + ('PyYAML', '5.1.2'), + ('Seaborn', '0.10.0', versionsuffix), + ('GitPython', '3.1.0', versionsuffix), ] use_pip = True @@ -32,6 +35,7 @@ exts_default_options = {'source_urls': [PYPI_SOURCE]} local_augur_preinstallopts = """sed -i'' 's/"matplotlib >=2.0,.*/"matplotlib >=2.0",/' setup.py && """ local_augur_preinstallopts += """sed -i'' 's/"cvxopt >=1.1.9,.*/"cvxopt >=1.1.9",/' setup.py && """ +local_augur_preinstallopts += """sed -i'' 's/"seaborn >=0.9.0,.*/"seaborn >=0.9.0",/' setup.py && """ exts_list = [ ('appdirs', '1.4.3', { @@ -44,19 +48,9 @@ exts_list = [ ('ConfigArgParse', '1.2.1', { 'checksums': ['f30736dcd4e00455ffe3087454799ccb7f9b61d765492dd4b35bbcd62379db12'], }), - ('cycler', '0.10.0', { - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), ('datrie', '0.8.2', { 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], }), - ('gitdb', '4.0.4', { - 'checksums': ['6f0ecd46f99bb4874e5678d628c3a198e2b4ef38daea2756a2bfd8df7dd5c1a5'], - }), - ('GitPython', '3.1.1', { - 'modulename': 'git', - 'checksums': ['6d4f10e2aaad1864bb0f17ec06a2c2831534140e5883c350d58b4e85189dab74'], - }), ('importlib-metadata', '1.6.0', { 'modulename': 'importlib_metadata', 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', @@ -75,9 +69,6 @@ exts_list = [ 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], }), - ('kiwisolver', '1.2.0', { - 'checksums': ['247800260cd38160c362d211dcaf4ed0f7816afb5efe56544748b21d6ad6d17f'], - }), ('nbformat', '5.0.5', { 'checksums': ['f0c47cf93c505cb943e2f131ef32b8ae869292b5f9f279db2bafb35867923f69'], }), @@ -91,19 +82,9 @@ exts_list = [ ('pyrsistent', '0.16.0', { 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], }), - ('PyYAML', '5.3.1', { - 'modulename': 'yaml', - 'checksums': ['b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d'], - }), ('ratelimiter', '1.2.0.post0', { 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], }), - ('seaborn', '0.9.1', { - 'checksums': ['da33aa8c20a9a342ce73831d02831a10413f54a05471c7f31edf34f225d456ae'], - }), - ('smmap', '3.0.2', { - 'checksums': ['b46d3fc69ba5f367df96d91f8271e8ad667a198d5a28e215a6c3d9acd133a911'], - }), ('snakemake', '5.10.0', { 'checksums': ['a3fa8b12db84938c919996d61be66031bcb99c4b4d017278731324a6112b0d59'], }), @@ -121,7 +102,7 @@ exts_list = [ 'source_urls': ['https://github.com/nextstrain/augur/archive/'], 'use_pip_extras': 'full', 'checksums': ['bf520dfc7fe2bf72e12c8de25cd97ca84686345fbb1c4a3456b060500c9c25b3'], - # Change augur strict dependency on matplotlib and cvxopt. Newer versions can be used. + # Change augur strict dependency on matplotlib, cvxopt and seaborn. Newer versions can be used. 'preinstallopts': local_augur_preinstallopts, }), ] From 2b5aa6ba17fdbde9307d2d70dba34853d9ef42d7 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 17 Apr 2020 10:53:17 +0200 Subject: [PATCH 123/431] Removed commented extensions --- .../Bio-EUtilities-1.76-GCCcore-8.3.0.eb | 30 ------------------- 1 file changed, 30 deletions(-) diff --git a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb index ddfd6cf5d09..dc41e894b84 100644 --- a/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bio-EUtilities/Bio-EUtilities-1.76-GCCcore-8.3.0.eb @@ -21,41 +21,11 @@ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ - # ('ExtUtils::MakeMaker', '7.44', { - # 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - # 'checksums': ['52a18f8271250faf5f3527499dd2b78d3b4fd3b064408d0cfdda9a3538887188'], - # }), - # ('IO::Handle', '1.42', { - # 'source_tmpl': 'IO-%(version)s.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], - # 'checksums': ['eec5cc33a6cddba8b5d2425b60752882add7e4d41b7431a0ea4dcd73cc1f8cca'], - # }), - # ('Test::More', '1.302171', { - # 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - # 'checksums': ['e27f90d2b2a6bc6ffa7675a072c2f41d5caffd99858dc69b2030940cc138368a'], - # }), ('Bio::ASN1::EntrezGene', '1.73', { 'source_tmpl': 'Bio-ASN1-EntrezGene-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], 'checksums': ['f9e778db705ce5c35ad2798e38a8490b644edfdc14253aa1b74a1f5e79fc6a4b'], }), - # ('Cwd', '3.75', { - # 'source_tmpl': 'PathTools-%(version)s.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - # 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], - # }), - # ('Data::Dumper', '2.173', { - # 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - # 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], - # }), - # ('LWP::UserAgent', '6.43', { - # 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', - # 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - # 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], - # }), ('Text::Wrap', '2013.0523', { 'source_tmpl': 'Text-Tabs+Wrap-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MU/MUIR/modules'], From 938e2cf5898834fd51171a21489eb9581ffbbab0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 11:42:55 +0200 Subject: [PATCH 124/431] run nosetests in correct directory in CVXOPT 1.2.4 easyconfig --- .../c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb index 641cd7e6584..103127af07d 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb @@ -36,6 +36,6 @@ preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_ installopts = ' --no-binary cvxopt' -sanity_check_commands = ['nosetests'] +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && nosetests'] moduleclass = 'math' From 505616652f72aa9c75ace6c3ec7d42822764f690 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zden=C4=9Bk=20Mat=C4=9Bj?= Date: Fri, 17 Apr 2020 12:15:09 +0200 Subject: [PATCH 125/431] Qt5-5.13.1-GCCcore-8.3.0: adding patch for undefined reference to 'qfloat16::mantissatable' --- .../q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb | 2 ++ .../q/Qt5/Qt5-5.13.1_fix-mantissatable.patch | 22 +++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-mantissatable.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb index fb55ae8948d..5eadc5a2d20 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb @@ -18,11 +18,13 @@ sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = [ 'Qt5-%(version)s_fix-avx2.patch', 'Qt5-%(version)s_fix-qmake-libdir.patch', + 'Qt5-%(version)s_fix-mantissatable.patch', ] checksums = [ 'adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e', # qt-everywhere-src-5.13.1.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch + 'cb23b917dd145b6775d7ffb3d8c143749d183d32972111f0c31133e41803f56b', # Qt5-5.13.1_fix-mantissatable.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-mantissatable.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-mantissatable.patch new file mode 100644 index 00000000000..7a89f17158d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-mantissatable.patch @@ -0,0 +1,22 @@ +replaces F16C preprocessor conditional directives in gen_qfloat16_tables.cpp +author: Zdenek Matej, fix taken from Qt5.14, see pr #10332 +--- qtbase/src/tools/qfloat16-tables/gen_qfloat16_tables.cpp ++++ qtbase/src/tools/qfloat16-tables/gen_qfloat16_tables.cpp +@@ -79,7 +79,7 @@ + fid.write("#include \n\n"); + + fid.write("QT_BEGIN_NAMESPACE\n\n"); +- fid.write("#if !defined(__F16C__) && !defined(__ARM_FP16_FORMAT_IEEE)\n\n"); ++ fid.write("#if !defined(__ARM_FP16_FORMAT_IEEE)\n\n"); + + fid.write("const quint32 qfloat16::mantissatable[2048] = {\n"); + fid.write("0,\n"); +@@ -156,7 +156,7 @@ + + fid.write("};\n\n"); + +- fid.write("#endif // !__F16C__ && !__ARM_FP16_FORMAT_IEEE\n\n"); ++ fid.write("#endif // !__ARM_FP16_FORMAT_IEEE\n\n"); + fid.write("QT_END_NAMESPACE\n"); + fid.close(); + return 0; From 029b7cae8564cd3b848729d2f65e0ca0974d6682 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 14:31:53 +0200 Subject: [PATCH 126/431] add Perl build dep for Autoconf/Automake using GCCcore/7.3.0 and GCCcore/8.2.0 toolchains (fixes #1822,#8704) --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb | 1 + easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb | 1 + .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb | 1 + .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb index e31a322aebd..2f16934eaba 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb @@ -22,6 +22,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] builddependencies = [ ('binutils', '2.30'), + ('Perl', '5.28.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb index a2d4749f3a0..344b858eb5e 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb @@ -22,6 +22,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] builddependencies = [ ('binutils', '2.31.1'), + ('Perl', '5.28.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb index 444c4e473a5..f51d3cdf739 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb @@ -27,6 +27,7 @@ checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] builddependencies = [ ('binutils', '2.30'), + ('Perl', '5.28.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb index c7562adcc26..051b452f6a1 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb @@ -27,6 +27,7 @@ checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] builddependencies = [ ('binutils', '2.31.1'), + ('Perl', '5.28.1'), ] dependencies = [ From ec1dcf6ef4ac78a1224c545c9b8fefb08b4e78d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 15:28:18 +0200 Subject: [PATCH 127/431] avoid introducing duplicate extensions in Perl 5.30.0 easyconfig --- .../easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb index 417ce82c1b6..3a92847cd5e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb @@ -1637,21 +1637,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], 'checksums': ['7af1c41de34b2e4dbff700a29d7387549c2b6cf16142214450c924707ddb0f82'], }), - ('LWP::UserAgent', '6.43', { - 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['e9849d7ee6fd0e89cc999e63d7612c951afd6aeea6bc721b767870d9df4ac40d'], - }), ('Mozilla::CA', '20180117', { 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], 'checksums': ['f2cc9fbe119f756313f321e0d9f1fac0859f8f154ac9d75b1a264c1afdf4e406'], }), - ('Net::HTTPS', '6.19', { - 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['52b76ec13959522cae64d965f15da3d99dcb445eddd85d2ce4e4f4df385b2fc4'], - }), ('Test::More', '1.302171', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], From 48018bb8625acf1654fb4871718a31260d5bc359 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 15:28:42 +0200 Subject: [PATCH 128/431] also add Mozilla::CA, Test::RequiresInternet and LWP::Protocol::https extensions to Perl 5.30.2 easyconfig --- .../p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index c6295da16ae..8a0d98ae4a8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -1617,11 +1617,26 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], 'checksums': ['7af1c41de34b2e4dbff700a29d7387549c2b6cf16142214450c924707ddb0f82'], }), + ('Mozilla::CA', '20180117', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], + 'checksums': ['f2cc9fbe119f756313f321e0d9f1fac0859f8f154ac9d75b1a264c1afdf4e406'], + }), ('Test::More', '1.302172', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['7388768f04128294a0e24c553eefbd2a464464617a8c19dfc21538ad5f4334fc'], }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN/'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('LWP::Protocol::https', '6.07', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['522cc946cf84a1776304a5737a54b8822ec9e79b264d0ba0722a70473dbfb9e7'], + }), ('Module::Load', '0.34', { 'source_tmpl': 'Module-Load-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], From 823158e2a1e3e7daebeed6a5bab8846609a616fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 15:38:22 +0200 Subject: [PATCH 129/431] use https:// URLs in homepage for Autoconf/Automake --- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb index 2f16934eaba..1fc62650b31 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Autoconf' version = '2.69' -homepage = 'http://www.gnu.org/software/autoconf/' +homepage = 'https://www.gnu.org/software/autoconf/' description = """ Autoconf is an extensible package of M4 macros that produce shell scripts diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb index 344b858eb5e..d7e71bcf1a8 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Autoconf' version = '2.69' -homepage = 'http://www.gnu.org/software/autoconf/' +homepage = 'https://www.gnu.org/software/autoconf/' description = """ Autoconf is an extensible package of M4 macros that produce shell scripts diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb index f51d3cdf739..f7edee6b6a7 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Automake' version = '1.16.1' -homepage = 'http://www.gnu.org/software/automake/automake.html' +homepage = 'https://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb index 051b452f6a1..20ed35318a8 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.2.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Automake' version = '1.16.1' -homepage = 'http://www.gnu.org/software/automake/automake.html' +homepage = 'https://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" From 2653aacb84692fee0c931225c13c3621b4f98a01 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Apr 2020 19:24:26 +0200 Subject: [PATCH 130/431] adding easyconfigs: nauty-2.6r12-GCC-8.2.0-2.31.1.eb --- .../n/nauty/nauty-2.6r12-GCC-8.2.0-2.31.1.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/nauty/nauty-2.6r12-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.6r12-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/n/nauty/nauty-2.6r12-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..ff021a070cf --- /dev/null +++ b/easybuild/easyconfigs/n/nauty/nauty-2.6r12-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'nauty' +version = '2.6r12' + +homepage = 'http://pallini.di.uniroma1.it/' +description = """nauty and Traces are programs for computing automorphism groups of graphs and +digraphs. They can also produce a canonical label.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['http://pallini.di.uniroma1.it'] +sources = ['nauty%s.tar.gz' % version.replace('.', '')] +checksums = ['862ae0dc3656db34ede6fafdb0999f7b875b14c7ab4fedbb3da4f28291eb95dc'] + +local_executables = [ + 'addedgeg', 'amtog', 'biplabg', 'catg', 'complg', 'converseg', 'copyg', 'countg', 'cubhamg', 'deledgeg', + 'delptg', 'directg', 'dreadnaut', 'dretodot', 'dretog', 'genbg', 'genbgL', 'geng', 'genquarticg', 'genrang', + 'genspecialg', 'gentourng', 'gentreeg', 'hamheuristic', 'labelg', 'linegraphg', 'listg', 'multig', 'newedgeg', + 'NRswitchg', 'pickg', 'planarg', 'ranlabg', 'shortg', 'showg', 'subdivideg', 'twohamg', 'vcolg', 'watercluster2' +] +local_headers = [ + 'gtools.h', 'gutils.h', 'naugroup.h', 'naugstrings.h', 'naurng.h', 'nausparse.h', 'nautaux.h', 'nautinv.h', + 'naututil.h', 'nauty.h', 'planarity.h', 'quarticirred28.h', 'rng.h', 'schreier.h', 'traces.h' +] +local_libs = ['nauty%s.a' % l for l in ['', '1', 'L', 'L1', 'W', 'W1']] + +prebuildopts = "./configure && " + +runtest = "checks" + +files_to_copy = [ + (local_executables, "bin"), + (local_headers, "include/%(name)s"), + (local_libs, "lib"), +] + +# prepend "lib" to library files to standarize their name +postinstallcmds = ["cd %%(installdir)s/lib/ && mv %s lib%s" % (l, l) for l in local_libs] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + + ['include/%%(name)s/%s' % h for h in local_headers] + + ['lib/lib%s' % l for l in local_libs], + 'dirs': [''] +} + +moduleclass = 'math' From f88f3042dee903888835d1557e6d830fc8e6d36c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Apr 2020 19:34:57 +0200 Subject: [PATCH 131/431] adding easyconfigs: Arb-2.16.0-GCC-8.2.0-2.31.1.eb, cddlib-0.94i-GCCcore-8.2.0.eb, CoCoALib-0.99601-GCC-8.2.0-2.31.1.eb, E-ANTIC-0.1.2-GCC-8.2.0-2.31.1.eb, FLINT-2.5.2-GCC-8.2.0-2.31.1.eb, nauty-2.7rc2-GCC-8.2.0-2.31.1.eb, Normaliz-3.7.4-gompi-2019a.eb --- .../a/Arb/Arb-2.16.0-GCC-8.2.0-2.31.1.eb | 35 +++++++++++++ .../CoCoALib-0.99601-GCC-8.2.0-2.31.1.eb | 44 ++++++++++++++++ .../c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb | 34 +++++++++++++ .../E-ANTIC/E-ANTIC-0.1.2-GCC-8.2.0-2.31.1.eb | 39 +++++++++++++++ .../f/FLINT/FLINT-2.5.2-GCC-8.2.0-2.31.1.eb | 34 +++++++++++++ .../n/Normaliz/Normaliz-3.7.4-gompi-2019a.eb | 46 +++++++++++++++++ .../n/nauty/nauty-2.7rc2-GCC-8.2.0-2.31.1.eb | 50 +++++++++++++++++++ 7 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99601-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-0.1.2-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/n/Normaliz/Normaliz-3.7.4-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/n/nauty/nauty-2.7rc2-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..95df88982ff --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.16.0' + +homepage = 'http://arblib.org/' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77464be4d34a511bb004457f862fec857ff934b0ed58d56d6f52d76ebadd4daf'] + +dependencies = [ + ('FLINT', '2.5.2'), + ('GMP', '6.1.2'), + ('MPFR', '4.0.2'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99601-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99601-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..b68bb3b9f89 --- /dev/null +++ b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99601-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'CoCoALib' +version = '0.99601' + +homepage = 'http://cocoa.dima.unige.it/cocoalib ' +description = "CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra." + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['http://cocoa.dima.unige.it/cocoalib/tgz'] +sources = [SOURCE_TGZ] +checksums = ['caf37f71398b9715be262e434f04a218db05cfa58e08bce954626d7f4ffd6b75'] + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('GMP', '6.1.2'), + ('cddlib', '0.94i'), # optional +] + +# Boost and libreadline only needed for CoCoA-5 +configopts = "--no-boost --no-readline --threadsafe-hack " +# Use cddlib from EB +configopts += "--with-libcddgmp=${EBROOTCDDLIB}/lib/libcddgmp.a " + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +# Makefile is not smart enough to create missing directories +preinstallopts = "mkdir %(installdir)s/{include,lib} && " + +# Move doc and examples from include to share +postinstallcmds = [ + "mkdir %(installdir)s/share", + "mv %(installdir)s/include/CoCoA-%(version)s/{doc,examples} %(installdir)s/share/", +] + +sanity_check_paths = { + 'files': ['lib/libcocoa.a'], + 'dirs': ['include/CoCoA-%(version)s', 'share/doc', 'share/examples'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..42defdbf051 --- /dev/null +++ b/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'cddlib' +version = '0.94i' + +homepage = 'https://github.com/cddlib/cddlib' +description = "An efficient implementation of the Double Description Method" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +github_account = 'cddlib' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c60dac8697357740c593f8f255d49ac8a5069623561d68720fd9089367c90f4a'] + +builddependencies = [('Autotools', '20180311')] + +dependencies = [('GMP', '6.1.2')] + +preconfigopts = "autoreconf -f -i && " + +buildopts = "SUBDIRS='lib-src src'" # build sources but spare the documentation in latex + +local_exes = ['adjacency', 'allfaces', 'fourier', 'lcdd', 'projection', 'redcheck', 'scdd', 'testcdd1', + 'testcdd2', 'testlp1', 'testlp2', 'testlp3', 'testshoot'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + ['bin/%s_gmp' % x for x in local_exes] + + ['lib/%s.%s' % (l, e) for l in ['libcdd', 'libcddgmp'] for e in ['a', SHLIB_EXT]] + + ['include/%s.h' % h for h in ['cdd', 'cddmp', 'cddtypes', 'setoper']], + 'dirs': [''] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-0.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-0.1.2-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..5995a5d6860 --- /dev/null +++ b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-0.1.2-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'E-ANTIC' +version = '0.1.2' + +homepage = 'https://github.com/videlec/e-antic' +description = """E-ANTIC is a C/C++ library to deal with real embedded number fields built on +top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as +possible exact arithmetic operations and comparisons.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +github_account = 'videlec' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b279686f099048f65755dbbbdf71d3b941d7bd993f6ccd37d5f2e14de3037e50'] + +builddependencies = [ + ('Autotools', '20180311'), +] + +dependencies = [ + ('FLINT', '2.5.2'), + ('Arb', '2.16.0'), +] + +preconfigopts = "autoreconf -f -i && " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['eantic', 'eanticxx'] for e in ['a', SHLIB_EXT]] + + ['include/e-antic/%s.h' % h for h in ['e-antic', 'nf', 'nf_elem', 'poly_extra', 'renf', + 'renf_elem', 'renfxx']], + 'dirs': ['share/doc'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..1e03ade2de4 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FLINT' +version = '2.5.2' + +homepage = 'http://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cbf1fe0034533c53c5c41761017065f85207a1b770483e98b2392315f6575e87'] + +dependencies = [ + ('GMP', '6.1.2'), + ('MPFR', '4.0.2'), +] + +configopts = '--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.7.4-gompi-2019a.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.7.4-gompi-2019a.eb new file mode 100644 index 00000000000..3825e2b2216 --- /dev/null +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.7.4-gompi-2019a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Normaliz' +version = '3.7.4' + +homepage = 'https://www.normaliz.uni-osnabrueck.de/' +description = """Normaliz is a open source tool for computations in affine monoids, vector +configurations, rational polyhedra and rational cones. Normaliz now computes +rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic +extensions of QQ.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c++11'} + +github_account = 'Normaliz' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1a33e7695d43ebc09c81c9d0192f304df71640baa3a9fd0c7552a0075b8a1da5'] + +builddependencies = [ + ('Autotools', '20180311'), +] + +dependencies = [ + ('Boost', '1.70.0'), + ('GMP', '6.1.2'), + ('CoCoALib', '0.99601'), + ('FLINT', '2.5.2'), + ('Arb', '2.16.0'), + ('E-ANTIC', '0.1.2'), + ('nauty', '2.7rc2'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = "--with-gmp=$EBROOTGMP --with-cocoalib=$EBROOTCOCOALIB --with-flint=$EBROOTFLINT " +configopts += "--with-e-antic=$EBROOTEMINANTIC --with-nautylib=$EBROOTNAUTY" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/normaliz'] + ['lib/libnormaliz.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/libnormaliz'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.7rc2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/n/nauty/nauty-2.7rc2-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..bc39e226559 --- /dev/null +++ b/easybuild/easyconfigs/n/nauty/nauty-2.7rc2-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'nauty' +version = '2.7rc2' + +homepage = 'http://pallini.di.uniroma1.it/' +description = """nauty and Traces are programs for computing automorphism groups of graphs and +digraphs. They can also produce a canonical label.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['http://pallini.di.uniroma1.it'] +sources = ['nauty%s.tar.gz' % version.replace('.', '')] +checksums = ['fe5b893579d84736a6e1383e0dfe95f9df55bff6ad3eaafd44660e08745ab32f'] + +local_executables = [ + 'addedgeg', 'amtog', 'assembleg', 'biplabg', 'catg', 'complg', 'converseg', 'copyg', 'countg', 'cubhamg', + 'deledgeg', 'delptg', 'directg', 'dreadnaut', 'dretodot', 'dretog', 'edgetransg', 'genbg', 'genbgL', 'geng', + 'gengL', 'genquarticg', 'genrang', 'genspecialg', 'gentourng', 'gentreeg', 'hamheuristic', 'labelg', 'linegraphg', + 'listg', 'multig', 'newedgeg', 'NRswitchg', 'pickg', 'planarg', 'ranlabg', 'shortg', 'showg', 'subdivideg', + 'twohamg', 'underlyingg', 'vcolg', 'watercluster2' +] +local_headers = [ + 'gtools.h', 'gutils.h', 'naugroup.h', 'naugstrings.h', 'naurng.h', 'nausparse.h', 'nautaux.h', 'nautinv.h', + 'naututil.h', 'nautycliquer.h', 'nauty.h', 'planarity.h', 'quarticirred28.h', 'rng.h', 'schreier.h', 'traces.h' +] +local_libs = ['nauty%s.a' % l for l in ['', '1', 'L', 'L1', 'W', 'W1']] + +prebuildopts = "./configure && " + +runtest = "checks" + +files_to_copy = [ + (local_executables, "bin"), + (local_headers, "include/%(name)s"), + (local_libs, "lib"), +] + +# prepend "lib" to library files to standarize their name +postinstallcmds = ["cd %%(installdir)s/lib/ && mv %s lib%s" % (l, l) for l in local_libs] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + + ['include/%%(name)s/%s' % h for h in local_headers] + + ['lib/lib%s' % l for l in local_libs], + 'dirs': [''] +} + +moduleclass = 'math' From c391b57c0a740f75c6043331b76153bf0c2390a3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Apr 2020 19:51:14 +0200 Subject: [PATCH 132/431] add build dependency on binutils to cddlib v0.94i --- easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb index 42defdbf051..1a250e40752 100644 --- a/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/cddlib/cddlib-0.94i-GCCcore-8.2.0.eb @@ -14,7 +14,10 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['c60dac8697357740c593f8f255d49ac8a5069623561d68720fd9089367c90f4a'] -builddependencies = [('Autotools', '20180311')] +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), +] dependencies = [('GMP', '6.1.2')] From 9b27cfaf77520458408c65aa062622a9c22cd2f3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Apr 2020 20:00:37 +0200 Subject: [PATCH 133/431] adding easyconfigs: Singular-4.1.2-GCC-8.2.0-2.31.1.eb, NTL-11.3.4-GCC-8.2.0-2.31.1.eb, 4ti2-1.6.9-GCC-8.2.0-2.31.1.eb --- .../0/4ti2/4ti2-1.6.9-GCC-8.2.0-2.31.1.eb | 30 +++++++++++ .../n/NTL/NTL-11.3.4-GCC-8.2.0-2.31.1.eb | 38 +++++++++++++ .../Singular-4.1.2-GCC-8.2.0-2.31.1.eb | 54 +++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.3.4-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/s/Singular/Singular-4.1.2-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..c7cd680d060 --- /dev/null +++ b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = '4ti2' +version = '1.6.9' + +homepage = 'https://4ti2.github.io/' +description = """A software package for algebraic, geometric and combinatorial problems on linear spaces""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +github_account = '4ti2' +source_urls = [GITHUB_SOURCE] +sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4'] + +dependencies = [ + ('GMP', '6.1.2'), + ('GLPK', '4.65'), +] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']], + 'dirs': ['include/4ti2', 'lib', 'share/4ti2'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/n/NTL/NTL-11.3.4-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..b80f9a76e06 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.3.4-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,38 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) + +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.3.4' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://shoup.net/ntl/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d93baa2a1c6c7477113dc71413dedf74bcc8d9477427c3d1097be68fa30be39'] + +dependencies = [ + ('GMP', '6.1.2'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Singular/Singular-4.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/Singular/Singular-4.1.2-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..efac733dba9 --- /dev/null +++ b/easybuild/easyconfigs/s/Singular/Singular-4.1.2-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'Singular' +version = '4.1.2' + +homepage = 'https://www.singular.uni-kl.de/' +description = """Singular is a computer algebra system for polynomial computations, +with special emphasis on commutative and non-commutative algebra, algebraic geometry, +and singularity theory.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Singular/Sources/archive'] +sources = ['Release-%s.tar.gz' % version.replace('.', '-')] +checksums = ['2193bc790a2a87e9fb1561fd527e30065da5985d8b0ad050b262e49ca38bb5aa'] + +builddependencies = [ + ('Autotools', '20180311'), + ('Doxygen', '1.8.15'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libreadline', '8.0'), + ('GMP', '6.1.2'), + ('MPFR', '4.0.2'), + ('FLINT', '2.5.2'), + ('NTL', '11.3.4'), + ('cddlib', '0.94i'), + ('4ti2', '1.6.9'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --with-flint=$EBROOTFLINT --with-ntl=$EBROOTNTL" + +# Disable man pages because the doc folder is missing in the source tarball (issue Singular/Sources#975) +local_disable_man = "dist_man1_MANS=''" + +buildopts = local_disable_man + +runtest = 'check %s' % local_disable_man + +installopts = local_disable_man + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ESingular', 'Singular', 'TSingular', 'libpolys-config', 'libsingular-config']] + + ['lib/lib%s.%s' % (l, e) for l in ['Singular', 'factory', 'gfan', 'omalloc', 'polys', 'singular_resources'] + for e in ['a', SHLIB_EXT]], + 'dirs': ['include/%s' % h for h in ['factory', 'gfanlib', 'omalloc', 'resources', 'singular']] + + ['libexec/singular', 'share'], +} + +moduleclass = 'math' From 9a5e5345e149571db96af04e2383ab6f5ce4d45f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Apr 2020 20:07:50 +0200 Subject: [PATCH 134/431] adding easyconfigs: lrslib-7.0a-gompi-2019a.eb, gap-4.11.0-foss-2019a.eb and patches: lrslib-7.0a-use-EB-values.patch --- .../g/gap/gap-4.11.0-foss-2019a.eb | 57 +++++ .../l/lrslib/lrslib-7.0a-gompi-2019a.eb | 38 +++ .../l/lrslib/lrslib-7.0a-use-EB-values.patch | 217 ++++++++++++++++++ 3 files changed, 312 insertions(+) create mode 100644 easybuild/easyconfigs/g/gap/gap-4.11.0-foss-2019a.eb create mode 100644 easybuild/easyconfigs/l/lrslib/lrslib-7.0a-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/l/lrslib/lrslib-7.0a-use-EB-values.patch diff --git a/easybuild/easyconfigs/g/gap/gap-4.11.0-foss-2019a.eb b/easybuild/easyconfigs/g/gap/gap-4.11.0-foss-2019a.eb new file mode 100644 index 00000000000..ad864ba10b6 --- /dev/null +++ b/easybuild/easyconfigs/g/gap/gap-4.11.0-foss-2019a.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'gap' +version = '4.11.0' + +homepage = 'https://www.gap-system.org' +description = """GAP is a system for computational discrete algebra, +with particular emphasis on Computational Group Theory.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gap-system.org/pub/gap/gap-%(version_major_minor)s/tar.gz/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6fda7af23394708aeb3b4bca8885f5fdcb7c3ae4419639dfb2d9f67d3f590abb'] + +unpack_options = '--strip-components=1' + +builddependencies = [ + ('Autotools', '20180311'), + ('Perl', '5.28.1'), # needed to install NormalizInterface +] + +dependencies = [ + ('GMP', '6.1.2'), + ('libreadline', '8.0'), + ('zlib', '1.2.11'), + ('4ti2', '1.6.9'), # needed by 4ti2Interface, HeLP + ('cddlib', '0.94i'), # needed by CddInterface + ('cURL', '7.63.0'), # needed by curlInterface + ('lrslib', '7.0a'), # needed by HeLP + ('ncurses', '6.1'), # needed by Browse + ('Normaliz', '3.7.4'), # needed by NormalizInterface, HeLP + ('Singular', '4.1.2'), # needed by singular + ('ZeroMQ', '4.3.2'), # needed by ZeroMQInterface +] + +# It doesn't have a working make install and hardcodes the build path +buildininstalldir = True +skipsteps = ['install'] + +# Disable bundled script to download and build Normaliz +prebuildopts = "sed -i 's|./build-normaliz.sh|#build-normaliz.sh|' bin/BuildPackages.sh && " +# BuildPackages.sh tries to build any GAP packages that require compilation +# If one fails due to missing dependencies, it's skipped automatically +buildopts = ' && cd pkg && ../bin/BuildPackages.sh' + +runtest = "testinstall" + +postinstallcmds = ["cd bin && ln -s gap.sh gap"] + +sanity_check_paths = { + 'files': ['bin/gap.sh', 'bin/gap', 'gap', 'gac'], + 'dirs': ['pkg'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.0a-gompi-2019a.eb b/easybuild/easyconfigs/l/lrslib/lrslib-7.0a-gompi-2019a.eb new file mode 100644 index 00000000000..84dab0e2ba6 --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.0a-gompi-2019a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'lrslib' +version = '7.0a' + +homepage = 'http://cgm.cs.mcgill.ca/~avis/C/lrs.html' +description = """lrslib is a self-contained ANSI C implementation of the +reverse search algorithm for vertex enumeration/convex hull problems""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/'] +sources = ['lrslib-0%(version_major)s%(version_minor)s.tar.gz'] +patches = ['lrslib-%(version)s-use-EB-values.patch'] +checksums = [ + 'd38cb8633e856398b461b35daa269d960c2c0e12b3df5725359dc3940b518e0c', # lrslib-070a.tar.gz + '05c695691b404ff5c7ab2179c3811ce1cd1727dd767fbef21353ff6e1a250132', # lrslib-7.0a-use-EB-values.patch +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +skipsteps = ['configure'] + +# Default built plus mplrs +buildopts = 'lrs redund lrsgmp mplrs CFLAGS="$CFLAGS"' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['lrs', 'lrsgmp', 'lrsnash', 'mplrs', 'mplrsgmp', 'redund', 'redundgmp']] + + ['lib/liblrs.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.0a-use-EB-values.patch b/easybuild/easyconfigs/l/lrslib/lrslib-7.0a-use-EB-values.patch new file mode 100644 index 00000000000..a34fa756dae --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.0a-use-EB-values.patch @@ -0,0 +1,217 @@ +# Fix makefile to use EB environment +# Ward Poelmans, Alex Domingo (Vrije Universiteit Brussel) +--- makefile.orig 2020-04-18 01:53:22.403951000 +0200 ++++ makefile 2020-04-18 01:52:16.444386000 +0200 +@@ -35,7 +35,7 @@ + INCLUDEDIR = /usr/local/include + LIBDIR = /usr/local/lib + +-CFLAGS = -O3 -Wall ++CFLAGS = $(OPTFLAGS) -Wall + SHLIB_CFLAGS = -fPIC + mpicxx=mpic++ + +@@ -48,28 +48,28 @@ + MPLRSOBJ64=lrslong1-mplrs.o lrslib1-mplrs.o lrslibgmp-mplrs.o lrsgmp-mplrs.o lrsdriver.o mplrs64.o + + lrs: ${LRSOBJ} +- $(CC) ${CFLAGS} -DMA -DB128 -L${LIBDIR} -o lrs ${LRSOBJ} -lgmp ++ $(CC) ${CFLAGS} -DMA -DB128 $(LDFLAGS) -o lrs ${LRSOBJ} -lgmp + + lrs64: ${LRSOBJ64} +- $(CC) ${CFLAGS} -DMA -L${LIBDIR} -o lrs ${LRSOBJ64} -lgmp ++ $(CC) ${CFLAGS} -DMA $(LDFLAGS) -o lrs ${LRSOBJ64} -lgmp + + redund: ${REDUNDOBJ} +- $(CC) ${CFLAGS} -DMA -DB128 -L${LIBDIR} -o redund ${REDUNDOBJ} -lgmp ++ $(CC) ${CFLAGS} -DMA -DB128 $(LDFLAGS) -o redund ${REDUNDOBJ} -lgmp + + redund64: ${REDUNDOBJ64} +- $(CC) ${CFLAGS} -DMA -L${LIBDIR} -o redund ${REDUNDOBJ64} -lgmp ++ $(CC) ${CFLAGS} -DMA $(LDFLAGS) -o redund ${REDUNDOBJ64} -lgmp + + lrs.o: lrs.c +- $(CC) ${CFLAGS} -DMA -DB128 -L${LIBDIR} -c -o lrs.o lrs.c ++ $(CC) ${CFLAGS} -DMA -DB128 $(LDFLAGS) -c -o lrs.o lrs.c + + lrs64.o: lrs.c +- $(CC) ${CFLAGS} -DMA -L${LIBDIR} -c -o lrs64.o lrs.c ++ $(CC) ${CFLAGS} -DMA $(LDFLAGS) -c -o lrs64.o lrs.c + + redund.o: redund.c +- $(CC) ${CFLAGS} -DMA -DB128 -L${LIBDIR} -c -o redund.o redund.c ++ $(CC) ${CFLAGS} -DMA -DB128 $(LDFLAGS) -c -o redund.o redund.c + + redund64.o: redund.c +- $(CC) ${CFLAGS} -DMA -L${LIBDIR} -c -o redund64.o redund.c ++ $(CC) ${CFLAGS} -DMA $(LDFLAGS) -c -o redund64.o redund.c + + lrslong1.o: lrslong.c lrslong.h + $(CC) ${CFLAGS} -DMA -DSAFE -DLRSLONG -c -o lrslong1.o lrslong.c +@@ -84,10 +84,10 @@ + $(CC) ${CFLAGS} -DMA -DSAFE -DB128 -DLRSLONG -c -o lrslib2.o lrslib.c + + lrslibgmp.o: lrslib.c lrslib.h +- $(CC) ${CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o lrslibgmp.o lrslib.c ++ $(CC) ${CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o lrslibgmp.o lrslib.c + + lrsgmp.o: lrsgmp.c lrsgmp.h +- $(CC) ${CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o lrsgmp.o lrsgmp.c ++ $(CC) ${CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o lrsgmp.o lrsgmp.c + + + lrslong1-mplrs.o: lrslong.c lrslong.h +@@ -103,25 +103,25 @@ + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -DMA -DSAFE -DB128 -DLRSLONG -DPLRS -c -o lrslib2-mplrs.o lrslib.c + + lrslibgmp-mplrs.o: lrslib.c lrslib.h +- $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS -I${INCLUDEDIR} -c -o lrslibgmp-mplrs.o lrslib.c ++ $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS $(CPPFLAGS) -c -o lrslibgmp-mplrs.o lrslib.c + + lrsgmp-mplrs.o: lrsgmp.c lrsgmp.h +- $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS -I${INCLUDEDIR} -c -o lrsgmp-mplrs.o lrsgmp.c ++ $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS $(CPPFLAGS) -c -o lrsgmp-mplrs.o lrsgmp.c + + mplrs.o: mplrs.c mplrs.h lrslib.h lrsgmp.h +- $(mpicxx) ${CFLAGS} -I${INCLUDEDIR} -DMA -DPLRS -DTIMES -DB128 -DSIGNALS -D_WITH_GETLINE -c -o mplrs.o mplrs.c ++ $(mpicxx) ${CFLAGS} $(CPPFLAGS) -DMA -DPLRS -DTIMES -DB128 -DSIGNALS -D_WITH_GETLINE -c -o mplrs.o mplrs.c + + mplrs64.o: mplrs.c mplrs.h lrslib.h lrsgmp.h +- $(mpicxx) ${CFLAGS} -I${INCLUDEDIR} -DMA -DPLRS -DTIMES -DSIGNALS -D_WITH_GETLINE -c -o mplrs64.o mplrs.c ++ $(mpicxx) ${CFLAGS} $(CPPFLAGS) -DMA -DPLRS -DTIMES -DSIGNALS -D_WITH_GETLINE -c -o mplrs64.o mplrs.c + + mplrs: ${MPLRSOBJ} mplrsgmp +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -Wno-write-strings -Wno-sign-compare -DPLRS -DMA -DB128 -L${LIBDIR} -o mplrs ${MPLRSOBJ} -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -Wno-write-strings -Wno-sign-compare -DPLRS -DMA -DB128 $(LDFLAGS) -o mplrs ${MPLRSOBJ} -lgmp + + mplrs64: ${MPLRSOBJ64} mplrsgmp +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -Wno-write-strings -Wno-sign-compare -DPLRS -DMA -L${LIBDIR} -o mplrs ${MPLRSOBJ64} -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -Wno-write-strings -Wno-sign-compare -DPLRS -DMA $(LDFLAGS) -o mplrs ${MPLRSOBJ64} -lgmp + + mplrsgmp: mplrs.c mplrs.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -DPLRS -DGMP -I${INCLUDEDIR} mplrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -o mplrsgmp -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -DPLRS -DGMP $(CPPFLAGS) mplrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -o mplrsgmp -lgmp + + mplrs1: mplrs.c mplrs.h lrslib.c lrslib.h lrslong.c lrslong.h lrsdriver.h lrsdriver.c + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -static-libstdc++ -DPLRS -DSAFE -DLRSLONG mplrs.c lrslib.c lrslong.c lrsdriver.c -o mplrs1 +@@ -135,59 +135,59 @@ + + flint: lrs.c lrslib.c lrslib.h lrsgmp.c lrsgmp.h + @test -d ${INCLUDEDIR}/flint || { echo ${INCLUDEDIR}/flint not found; exit 1; } +- $(CC) -O3 -DFLINT -I${INCLUDEDIR} -I${INCLUDEDIR}/flint lrs.c lrsdriver.c lrslib.c lrsgmp.c -L${LIBDIR} -lflint -o lrsflint -lgmp ++ $(CC) $(OPTFLAGS) -DFLINT $(CPPFLAGS) $(CPPFLAGS)/flint lrs.c lrsdriver.c lrslib.c lrsgmp.c $(LDFLAGS) -lflint -o lrsflint -lgmp + + mplrsflint: mplrs.c mplrs.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.c lrsdriver.h +- ${mpicxx} ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DFLINT -Wno-write-strings -Wno-sign-compare -I${INCLUDEDIR}/flint -DPLRS -o mplrsflint mplrs.c lrsdriver.c lrslib.c lrsgmp.c -L${LIBDIR} -lflint -lgmp ++ ${mpicxx} ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DFLINT -Wno-write-strings -Wno-sign-compare $(CPPFLAGS)/flint -DPLRS -o mplrsflint mplrs.c lrsdriver.c lrslib.c lrsgmp.c $(LDFLAGS) -lflint -lgmp + + #comment out lines with -DB128 if __int128 not supported by your C compiler + + lrsgmp: lrs.c lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c redund.c +- gcc -O3 -DGMP -I${INCLUDEDIR} -o lrsgmp lrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -lgmp +- $(CC) -O3 -DGMP -I${INCLUDEDIR} redund.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -lgmp -o redundgmp ++ gcc $(OPTFLAGS) -DGMP $(CPPFLAGS) -o lrsgmp lrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -lgmp ++ $(CC) $(OPTFLAGS) -DGMP $(CPPFLAGS) redund.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -lgmp -o redundgmp + + single: lrs.c lrslong.c lrslong.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(CC) -O3 -DSAFE -DLRSLONG -o lrs1 lrs.c lrslib.c lrslong.c lrsdriver.c +- $(CC) -O3 -DLRSLONG -o lrs1n lrs.c lrslib.c lrslong.c lrsdriver.c +- $(CC) -O3 -DB128 -DSAFE -DLRSLONG -o lrs2 lrs.c lrslib.c lrslong.c lrsdriver.c +- $(CC) -O3 -DB128 -DLRSLONG -o lrs2n lrs.c lrslib.c lrslong.c lrsdriver.c +- $(CC) -O3 -DSAFE -DLRSLONG redund.c lrslib.c lrslong.c lrsdriver.c -o redund1 +- $(CC) -O3 -DB128 -DSAFE -DLRSLONG -DB128 redund.c lrslib.c lrslong.c lrsdriver.c -o redund2 ++ $(CC) $(OPTFLAGS) -DSAFE -DLRSLONG -o lrs1 lrs.c lrslib.c lrslong.c lrsdriver.c ++ $(CC) $(OPTFLAGS) -DLRSLONG -o lrs1n lrs.c lrslib.c lrslong.c lrsdriver.c ++ $(CC) $(OPTFLAGS) -DB128 -DSAFE -DLRSLONG -o lrs2 lrs.c lrslib.c lrslong.c lrsdriver.c ++ $(CC) $(OPTFLAGS) -DB128 -DLRSLONG -o lrs2n lrs.c lrslib.c lrslong.c lrsdriver.c ++ $(CC) $(OPTFLAGS) -DSAFE -DLRSLONG redund.c lrslib.c lrslong.c lrsdriver.c -o redund1 ++ $(CC) $(OPTFLAGS) -DB128 -DSAFE -DLRSLONG -DB128 redund.c lrslib.c lrslong.c lrsdriver.c -o redund2 + make lrsgmp + make redundgmp + + @test -d ${INCLUDEDIR}/flint || { echo ${INCLUDEDIR}/flint not found: lrsflint not created; exit 1; } +- $(CC) -O3 -DFLINT -I${INCLUDEDIR}/flint lrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -lflint -o lrsflint -lgmp +- $(CC) -O3 -DFLINT -I${INCLUDEDIR}/flint redund.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -lflint -o redundflint -lgmp ++ $(CC) $(OPTFLAGS) -DFLINT $(CPPFLAGS)/flint lrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -lflint -o lrsflint -lgmp ++ $(CC) $(OPTFLAGS) -DFLINT $(CPPFLAGS)/flint redund.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -lflint -o redundflint -lgmp + + + + allmp: lrs.c lrslib.c lrslib.h lrsmp.c lrsmp.h lrsdriver.h lrsdriver.c +- $(CC) -Wall -O3 -o lrs lrs.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -Wall -O3 -DLRSLONG -o lrs1 lrs.c lrslib.c lrsdriver.c lrslong.c +- $(CC) -O3 -o redund redund.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -O3 -DLRSLONG -o redund1 redund.c lrslib.c lrsdriver.c lrslong.c +- $(CC) -O3 -DLRS_QUIET -o lrsnash lrsnash.c lrsnashlib.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -O3 -o setnash setupnash.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -O3 -o setnash2 setupnash2.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -O3 -o 2nash 2nash.c ++ $(CC) -Wall $(OPTFLAGS) -o lrs lrs.c lrslib.c lrsdriver.c lrsmp.c ++ $(CC) -Wall $(OPTFLAGS) -DLRSLONG -o lrs1 lrs.c lrslib.c lrsdriver.c lrslong.c ++ $(CC) $(OPTFLAGS) -o redund redund.c lrslib.c lrsdriver.c lrsmp.c ++ $(CC) $(OPTFLAGS) -DLRSLONG -o redund1 redund.c lrslib.c lrsdriver.c lrslong.c ++ $(CC) $(OPTFLAGS) -DLRS_QUIET -o lrsnash lrsnash.c lrsnashlib.c lrslib.c lrsdriver.c lrsmp.c ++ $(CC) $(OPTFLAGS) -o setnash setupnash.c lrslib.c lrsdriver.c lrsmp.c ++ $(CC) $(OPTFLAGS) -o setnash2 setupnash2.c lrslib.c lrsdriver.c lrsmp.c ++ $(CC) $(OPTFLAGS) -o 2nash 2nash.c + + demo: lpdemo1.c lrslib.c lrsdriver.c lrslib.h lrsgmp.c lrsgmp.h +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo1 lpdemo1.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo lpdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo2 lpdemo2.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o vedemo vedemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o lpdemo1 lpdemo1.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o lpdemo lpdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o lpdemo2 lpdemo2.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o vedemo vedemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP + + lrsnash: lrsnash.c nashdemo.c lrsnashlib.c lrslib.c lrsnashlib.h lrslib.h lrsgmp.c lrsgmp.h lrslong.h lrsdriver.h lrsdriver.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnashgmp lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash1 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash2 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE -DB128 +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o nashdemo nashdemo.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o 2nash 2nash.c ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o lrsnashgmp lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o lrsnash1 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o lrsnash2 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE -DB128 ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o nashdemo nashdemo.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) $(OPTFLAGS) $(CPPFLAGS) $(LDFLAGS) -o 2nash 2nash.c + cp lrsnashgmp lrsnash + + fourier: fourier.c lrslib.h lrslib.c lrsgmp.h lrsgmp.c +- $(CC) -O3 -DGMP -I${INCLUDEDIR} fourier.c lrslib.c lrsdriver.c lrsgmp.c -L${LIBDIR} -lgmp -o fourier ++ $(CC) $(OPTFLAGS) -DGMP $(CPPFLAGS) fourier.c lrslib.c lrsdriver.c lrsgmp.c $(LDFLAGS) -lgmp -o fourier + + ###################################################################### + # From here on the author is David Bremner to whom you should turn for help +@@ -201,7 +201,7 @@ + SHLIBOBJ=lrslong1-shr.o lrslong2-shr.o lrslib1-shr.o lrslib2-shr.o \ + lrslibgmp-shr.o lrsgmp-shr.o lrsdriver-shr.o + +-SHLIBBIN=lrs-shared redund-shared lrsnash-shared ++SHLIBBIN=lrs-shared redund-shared lrsnash-shared mplrs lrsgmp mplrsgmp redundgmp + + # Building (linking) the shared library, and relevant symlinks. + +@@ -225,7 +225,7 @@ + $(CC) redund.o -o $@ -L . -llrs + + lrsnash-shared: ${SHLINK} lrsnash.c +- $(CC) -DGMP -DMA lrsnash.c lrsnashlib.c -I${INCLUDEDIR} -o $@ -L . -llrs -lgmp ++ $(CC) -DGMP -DMA lrsnash.c lrsnashlib.c $(CPPFLAGS) -o $@ -L . -llrs -lgmp + + # build object files for the shared library + +@@ -242,10 +242,10 @@ + $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DSAFE -DB128 -DLRSLONG -c -o $@ lrslong.c + + lrslibgmp-shr.o: lrslib.c lrslib.h +- $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o $@ lrslib.c ++ $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o $@ lrslib.c + + lrsgmp-shr.o: lrsgmp.c lrsgmp.h +- $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o $@ lrsgmp.c ++ $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o $@ lrsgmp.c + + lrslib2-shr.o: lrslib.c lrslib.h + $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DSAFE -DB128 -DLRSLONG -c -o $@ lrslib.c From 0d54d8ff5832f720ed11bf8dedab1c9e0e578af6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 20 Apr 2020 15:47:14 +0950 Subject: [PATCH 135/431] adding easyconfigs: SRA-Toolkit-2.10.5-centos_linux64.eb --- .../SRA-Toolkit-2.10.5-centos_linux64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.5-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.5-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.5-centos_linux64.eb new file mode 100644 index 00000000000..e0f6a43f6f7 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.10.5-centos_linux64.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# @author: Adam Huffman - The Francis Crick Institute +# Based on work by npklein +# +# updated to version 2.10.5 by +# @author: Rob Qiao - DeepThought HPC - https://staff.flinders.edu.au/research/deep-thought + +easyblock = 'PackedBinary' + +name = 'SRA-Toolkit' +version = '2.10.5' +versionsuffix = '-centos_linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = SYSTEM + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['ce93b1edabc2d5880605d66415a32a497351779129e5e9f5a0ea245a659399aa'] +sanity_check_paths = { + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] +} + +moduleclass = 'bio' From 8d7c34fa56e723eb3996d7e65c2c519d51ea3a86 Mon Sep 17 00:00:00 2001 From: ubuntu Date: Mon, 20 Apr 2020 06:29:07 +0000 Subject: [PATCH 136/431] adding easyconfigs: Salmon-1.2.0-gompi-2019b.eb --- .../s/Salmon/Salmon-1.2.0-gompi-2019b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb new file mode 100644 index 00000000000..486ec7aabdd --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb @@ -0,0 +1,49 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Jordi Blasco +# License:: GPL-v3.0 +# Based on Robert Qiao contribution +# # + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.2.0' + +homepage = 'https://salmon.readthedocs.io' +description = """Salmon is a wicked-fast program to produce a highly-accurate, +transcript-level quantification estimates from RNA-seq data. Salmon achieves +its accuracy and speed via a number of different innovations, including the use +of selective-alignment, and massively-parallel stochastic collapsed variational +inference.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'COMBINE-lab' +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c8a6647484ff630e4958aa4540cba28c0913b26922313876d747aba65eefb96f'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('pkg-config', '0.29.2'), + ('jemalloc', '5.2.1'), + ('Boost', '1.71.0'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('tbb', '2019_U9'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/salmon', 'lib/libsalmon_core.a'], + 'dirs': [], +} + +moduleclass = 'bio' From 6185c2c6d1294f7531275449e759466b4e1790d3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 20 Apr 2020 09:28:36 +0200 Subject: [PATCH 137/431] Use single-letter vars in list comprehension --- easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb index 75ffc099a04..fed53023160 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb @@ -49,10 +49,7 @@ local_adapters = [ sanity_check_paths = { 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h'] + - [ - 'lib/libscorep_adapter_%s.%s' % (local_adapter, local_ext) - for local_adapter in local_adapters for local_ext in ('a', SHLIB_EXT) - ], + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], 'dirs': [], } sanity_check_commands = ['scorep-config --help'] From cba5c8441e12cb36c4f0155e306e0a2696b387f7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Apr 2020 11:05:08 +0200 Subject: [PATCH 138/431] Alpha: switch to new install-type option from tarball --- .../a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb index 9c7d3b8eac6..afa0812925f 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb @@ -41,7 +41,7 @@ components = [ 'sources': [{'download_filename': '%s.zip' % local_pyinc_commit, 'filename': '%(name)s-%(version)s.zip'}], 'checksums': ['9dc9b2bafbfe7a694ff4025164dc6e356989ee89b914691457fb0a474fe66c9e'], 'start_dir': 'thekswenson-%%(name)s-%s' % local_pyinc_commit, - 'install_in_subdir': True, + 'install_type': 'subdir', }), (name, version, { 'easyblock': 'Tarball', @@ -53,7 +53,7 @@ components = [ '342d5d37bcfc19a2487c3b08860adc4246736919948b1968f899b0c595d7125d', # Alpha-20190607_fix-email.patch ], 'start_dir': 'thekswenson-%%(namelower)s-%s' % local_alpha_commit, - 'install_in_subdir': True, + 'install_type': 'subdir', 'keepsymlinks': True, }), ] From 8f2329b2d5d17a7bb426cccd632a18f3c723fe0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2020 13:30:03 +0200 Subject: [PATCH 139/431] adding easyconfigs: GffCompare-0.11.6-GCCcore-8.3.0.eb --- .../GffCompare-0.11.6-GCCcore-8.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..cde06a619f9 --- /dev/null +++ b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GffCompare' +version = '0.11.6' + +homepage = 'https://github.com/gpertea/gffcompare' +description = """GffCompare provides classification and reference annotation mapping and + matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6095d97301a9c8dbd5e99e8c42860ce5953546277a09a0b46c835019815f6174'] + +builddependencies = [('binutils', '2.32')] + +buildopts = " release" + +files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' From ad899300cb9df8e1020dce4c2722dbbb3f091ac3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Apr 2020 13:55:27 +0200 Subject: [PATCH 140/431] mention http:// Pfam website rather than ftp:// in load message of BiG-SCAPE easyconfig --- .../b/BiG-SCAPE/BiG-SCAPE-1.0.1-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.0.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.0.1-intel-2019b-Python-3.7.4.eb index 6a9ce301b4d..44b3b2cf910 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.0.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.0.1-intel-2019b-Python-3.7.4.eb @@ -42,7 +42,7 @@ modextrapaths = {'PATH': ''} modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website" -modloadmsg += "(ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" moduleclass = 'bio' From 023d2c8cd76e08b9f3a3d4b5fd58dfe6891c94f9 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Tue, 21 Apr 2020 17:27:54 +1200 Subject: [PATCH 141/431] Update Salmon-1.2.0-gompi-2019b.eb --- easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb index 486ec7aabdd..98e93d3807c 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb @@ -11,7 +11,7 @@ easyblock = 'CMakeMake' name = 'Salmon' version = '1.2.0' -homepage = 'https://salmon.readthedocs.io' +homepage = 'https://salmon.readthedocs.io' description = """Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use From e4ab979ce0afad9f23d098380a0a7ca723c8bf3e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 22 Apr 2020 02:00:35 +0200 Subject: [PATCH 142/431] adding easyconfigs: libuv-1.37.0-GCCcore-8.3.0.eb --- .../l/libuv/libuv-1.37.0-GCCcore-8.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libuv/libuv-1.37.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libuv/libuv-1.37.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libuv/libuv-1.37.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..5bcf426e69c --- /dev/null +++ b/easybuild/easyconfigs/l/libuv/libuv-1.37.0-GCCcore-8.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libuv' +version = '1.37.0' + +homepage = 'https://libuv.org' +description = "libuv is a multi-platform support library with a focus on asynchronous I/O." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +github_account = 'libuv' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['7afa3c8a326b3eed02a9addb584ae7e995ae4d30516cad5e1e4af911931162a6'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +preconfigopts = './autogen.sh; ' + +sanity_check_paths = { + 'files': ['include/uv.h', 'lib/libuv.a', 'lib/libuv.%s' % SHLIB_EXT, 'lib/pkgconfig/libuv.pc'], + 'dirs': [] +} + +moduleclass = 'lib' From 4d82df6945685f632efc64d1824f22fb8a55a1b9 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 22 Apr 2020 02:02:17 +0200 Subject: [PATCH 143/431] adding easyconfigs: utf8proc-2.5.0-GCCcore-8.3.0.eb --- .../utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..ecb83d6d114 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.5.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4e8dfc898cfd062493cb7f42d95d70ccdd3a4cd4d90bec0c71b47cca688f1be'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From bc9a357dc383607d23abffa4973786f89aa9b11b Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 22 Apr 2020 07:54:34 +0000 Subject: [PATCH 144/431] adding easyconfigs: DCMTK-3.6.5-GCCcore-8.3.0.eb --- .../d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0e5d21752d2 --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.5' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dicom.offis.de/download/dcmtk/dcmtk%s/' % version.replace('.', '')] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a05178665f21896dbb0974106dba1ad144975414abd760b4cf8f5cc979f9beb9'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.3'), + ('LibTIFF', '4.1.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.9'), + ('libiconv', '1.16'), +] + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +moduleclass = 'data' From 43948445aeab47a8b4e14e4eefa53268e8156133 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 09:55:01 +0200 Subject: [PATCH 145/431] enable enhance_sanity_check in LAMMPS easyconfigs (cfr. https://github.com/easybuilders/easybuild-framework/pull/3288) --- .../l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb | 2 ++ .../l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 2 ++ .../l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb | 2 ++ .../l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb | 2 ++ 4 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index 92d59f7fb16..33114ef66ee 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -91,6 +91,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +enhance_sanity_check = True + # run short test case to make sure installation doesn't produce blatently incorrect results; # this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 5db45529939..8bd37bde816 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -95,6 +95,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +enhance_sanity_check = True + # run short test case to make sure installation doesn't produce blatently incorrect results; # this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index 9deb6f6138b..404666e2679 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -91,6 +91,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +enhance_sanity_check = True + # run short test case to make sure installation doesn't produce blatently incorrect results; # this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index 74be8e3fe61..d89e7f66dc0 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -95,6 +95,8 @@ user_packages = [ 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', ] +enhance_sanity_check = True + # run short test case to make sure installation doesn't produce blatently incorrect results; # this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] From fd06eeaf39eee12f4d25a860d2e68c640ab21a01 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 22 Apr 2020 08:10:55 +0000 Subject: [PATCH 146/431] Adjust version of LibTIFF dependency --- easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb index 0e5d21752d2..421184f762a 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.5-GCCcore-8.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.3'), - ('LibTIFF', '4.1.0'), + ('LibTIFF', '4.0.10'), ('libpng', '1.6.37'), ('libxml2', '2.9.9'), ('libiconv', '1.16'), From fc695b381cd224d3b1a403a5dd2bff716b04f5fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 10:48:13 +0200 Subject: [PATCH 147/431] {data}[intel/2018b] PyTables v3.4.4, numexpr v2.6.5, LZO v2.10 w/ Python 3.6.6 --- .../l/LZO/LZO-2.10-GCCcore-7.3.0.eb | 36 ++++++++++++++ .../numexpr-2.6.5-intel-2018b-Python-3.6.6.eb | 23 +++++++++ ...PyTables-3.4.4-intel-2018b-Python-3.6.6.eb | 47 +++++++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..8dd300be9cc --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-7.3.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.30')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..b2c64126c55 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,23 @@ +name = 'numexpr' +version = '2.6.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://numexpr.readthedocs.io' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fe78a78e002806e87e012b6105f3b3d52d47fc7a72bafb56341fcec7ce02cfd7'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..486e268d94e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pyTables-3.4.2-fix-libs.patch'] +checksums = [ + 'c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114', # v3.4.4.tar.gz + 'f34a05573e7843e67dab011bede8436074362041747c028b409fac9f599231a3', # pyTables-3.4.2-fix-libs.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('numexpr', '2.6.5', versionsuffix), + ('HDF5', '1.10.2'), + ('LZO', '2.10'), + ('Blosc', '1.14.4'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_pip_check = True + +moduleclass = 'data' From 35d6300fdae216288f7f594eddfa60d5d7e7ec48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 13:27:13 +0200 Subject: [PATCH 148/431] use https:// in homepage in PyTables easyconfig --- .../p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb index 486e268d94e..bc7fcf8d684 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-intel-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'PyTables' version = '3.4.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.pytables.org' +homepage = 'https://www.pytables.org' description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical From bc93702c89b926813265f3d0500d2f560b3d6ce4 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 22 Apr 2020 14:33:03 +0200 Subject: [PATCH 149/431] Create Anaconda3-2020.02.eb upgrade to Anaconda3 version 2020.02 --- .../a/Anaconda3/Anaconda3-2020.02.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.02.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.02.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.02.eb new file mode 100644 index 00000000000..7032284df9e --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.02.eb @@ -0,0 +1,22 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10, 2020.20 by Joachim Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2020.02' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['2b9f088b2022edb474915d9f69a803d6449d5fdb4c303041f60ac4aefcc208bb'] + +moduleclass = 'lang' From b3a18bdab8c53f03f92c441767e3c20f5e8d8b05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 18:09:57 +0200 Subject: [PATCH 150/431] fix source_urls in ICU easyconfigs --- easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb index 69d4263c64c..4b11ded535a 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-6.4.0.eb @@ -10,7 +10,7 @@ description = """ICU is a mature, widely used set of C/C++ and Java libraries pr toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] checksums = ['d007f89ae8a2543a53525c74359b65b36412fa84b3349f1400be6dcf409fafef'] diff --git a/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-7.3.0.eb index 5ab07a8068c..861f3c35e68 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-61.1-GCCcore-7.3.0.eb @@ -10,7 +10,7 @@ description = """ICU is a mature, widely used set of C/C++ and Java libraries pr toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] checksums = ['d007f89ae8a2543a53525c74359b65b36412fa84b3349f1400be6dcf409fafef'] diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb index 337832d9009..95582ba5614 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb @@ -10,7 +10,7 @@ description = """ICU is a mature, widely used set of C/C++ and Java libraries pr toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] From fbe14e43b6a0052b959d2d004ab52b60b90e7338 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 18:30:15 +0200 Subject: [PATCH 151/431] also fix hardcoding of $CC to g++ in auxprogs/joingenes/Makefile subdirectory for AUGUSTUS 3.3.3 --- .../easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb | 2 +- .../a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb index 6162ef6e897..1570c025c64 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb @@ -21,7 +21,7 @@ patches = [ ] checksums = [ '2fc5f9fd2f0c3bba2924df42ffaf55b5c130228cea18efdb3b6dfab9efa8c9f4', # v3.3.3.tar.gz - '1e158b2241aa86077ae3b1b13ec7f26fbaf3fc49632afdc564fab88ac897e9a0', # AUGUSTUS-3.3.3_fix-hardcoding.patch + 'e2bb1206ebdde6aa344889563a6432cb1537800f2b5d3c7033152b21db724596', # AUGUSTUS-3.3.3_fix-hardcoding.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch index 6d447bb39e2..46450f01614 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch @@ -109,3 +109,11 @@ diff Augustus-3.3.3/auxprogs/filterBam/src/Makefile{.orig,} -ru INCLUDES = -I$(BAMTOOLS) -Iheaders -I./bamtools LIBS = -lbamtools -lz CFLAGS = -std=c++0x +--- Augustus-3.3.3/auxprogs/joingenes/Makefile.orig 2020-04-22 17:23:34.829927330 +0200 ++++ Augustus-3.3.3/auxprogs/joingenes/Makefile 2020-04-22 17:24:14.881206231 +0200 +@@ -1,4 +1,4 @@ +-CC=g++ ++CC=$(CXX) + CFLAGS=-Wall -std=gnu++0x + + all: joingenes From ce2bcaf69aabd0b6f1ed73f08740277c33699785 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 18:34:53 +0200 Subject: [PATCH 152/431] add easyconfig for AUGUSTUS 3.3.3 with intel/2019b toolchain --- .../a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb | 63 +++++++++++++++++++ .../BCFtools-1.10.2-iccifort-2019.5.281.eb | 38 +++++++++++ .../lpsolve-5.5.2.5-iccifort-2019.5.281.eb | 33 ++++++++++ 3 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.10.2-iccifort-2019.5.281.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb new file mode 100644 index 00000000000..70d72eefc98 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb @@ -0,0 +1,63 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.3.3' + +# HTTPS doesn't work +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'intel', 'version': '2019b'} + +# https://github.com/Gaius-Augustus/Augustus/archive +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix-hardcoding.patch', +] +checksums = [ + '2fc5f9fd2f0c3bba2924df42ffaf55b5c130228cea18efdb3b6dfab9efa8c9f4', # v3.3.3.tar.gz + 'e2bb1206ebdde6aa344889563a6432cb1537800f2b5d3c7033152b21db724596', # AUGUSTUS-3.3.3_fix-hardcoding.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.71.0'), + ('GSL', '2.6'), + ('SAMtools', '1.10'), + ('HTSlib', '1.10.2'), # also provides tabix + ('BCFtools', '1.10.2'), + ('lpsolve', '5.5.2.5'), + ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), + ('BamTools', '2.5.1'), + ('SQLite', '3.29.0'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', + 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.10.2-iccifort-2019.5.281.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.10.2-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..3ff051a119b --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.10.2-iccifort-2019.5.281.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.10.2' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c'] + +dependencies = [ + ('zlib', '1.2.11'), + ('HTSlib', '1.10.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.4'), + ('GSL', '2.6'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2019.5.281.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..88882776bf9 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2019.5.281.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.5' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' From e347bc34552b1e0a5d2e94f3621cb131bb2ae7fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 20:51:12 +0200 Subject: [PATCH 153/431] {tools}[foss/2019b] pysndfx v0.3.6, SoX v14.4.2 w/ Python 3.7.4 --- .../pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb | 27 +++++++++++++++++++ .../easyconfigs/s/SoX/SoX-14.4.2-GCC-8.3.0.eb | 22 +++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0d53be51dfc --- /dev/null +++ b/easybuild/easyconfigs/p/pysndfx/pysndfx-0.3.6-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pysndfx' +version = '0.3.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/carlthome/python-audio-effects' +description = """A lightweight Python wrapper for SoX - Sound eXchange. + Supported effects range from EQ and compression to phasers, reverb and pitch shifters.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ce168812963e398e849ad60aa1dc74e78f452ce0c948679367b2627459f39c9c'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('SoX', '14.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-8.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-8.3.0.eb new file mode 100644 index 00000000000..4b20f77fc7c --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-8.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'https://sourceforge.net/projects/sox' +description = """SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files + to other popular audio file types and also apply sound effects and filters during the conversion.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/rec', 'bin/sox', 'bin/soxi', 'include/sox.h', + 'lib/libsox.a', 'lib/libsox.%s' % SHLIB_EXT, 'lib/pkgconfig/sox.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'tools' From 6373c3aa3c28750b84f6aa9ddd4612cdad4ab6a9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Apr 2020 23:26:09 +0200 Subject: [PATCH 154/431] fix more hardcoded settings in AUGUSTUS v3.3.3 --- .../a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb | 2 +- .../a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb | 2 +- .../AUGUSTUS-3.3.3_fix-hardcoding.patch | 33 +++++++++++++++++++ 3 files changed, 35 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb index 1570c025c64..a6b55055cc5 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb @@ -21,7 +21,7 @@ patches = [ ] checksums = [ '2fc5f9fd2f0c3bba2924df42ffaf55b5c130228cea18efdb3b6dfab9efa8c9f4', # v3.3.3.tar.gz - 'e2bb1206ebdde6aa344889563a6432cb1537800f2b5d3c7033152b21db724596', # AUGUSTUS-3.3.3_fix-hardcoding.patch + '414907ab65cd27df33508f7d0c2fde4cc5e6ffd9fb7be9357d1488851e480e94', # AUGUSTUS-3.3.3_fix-hardcoding.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb index 70d72eefc98..47da0b5a46e 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb @@ -21,7 +21,7 @@ patches = [ ] checksums = [ '2fc5f9fd2f0c3bba2924df42ffaf55b5c130228cea18efdb3b6dfab9efa8c9f4', # v3.3.3.tar.gz - 'e2bb1206ebdde6aa344889563a6432cb1537800f2b5d3c7033152b21db724596', # AUGUSTUS-3.3.3_fix-hardcoding.patch + '414907ab65cd27df33508f7d0c2fde4cc5e6ffd9fb7be9357d1488851e480e94', # AUGUSTUS-3.3.3_fix-hardcoding.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch index 46450f01614..09a4623ecb0 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch @@ -117,3 +117,36 @@ diff Augustus-3.3.3/auxprogs/filterBam/src/Makefile{.orig,} -ru CFLAGS=-Wall -std=gnu++0x all: joingenes +--- Augustus-3.3.3/src/Makefile.orig 2020-04-22 22:28:10.074833000 +0200 ++++ Augustus-3.3.3/src/Makefile 2020-04-22 22:28:26.352479069 +0200 +@@ -24,7 +24,7 @@ + ifdef COMPGENEPRED + CXXFLAGS += -std=c++11 -DCOMPGENEPRED + endif +-INCLS = -I../include ++INCLS = ${CPPFLAGS} -I../include + + OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ + types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o \ +--- Augustus-3.3.3/auxprogs/utrrnaseq/Debug/makefile.orig 2020-04-22 23:04:30.186338000 +0200 ++++ Augustus-3.3.3/auxprogs/utrrnaseq/Debug/makefile 2020-04-22 23:04:57.667110000 +0200 +@@ -44,7 +44,7 @@ + utrrnaseq: $(OBJS) $(USER_OBJS) + @echo 'Building target: $@' + @echo 'Invoking: GCC C++ Linker' +- g++ -o "utrrnaseq" $(OBJS) $(USER_OBJS) $(LIBS) ++ $(CXX) $(CXXFLAGS) -o "utrrnaseq" $(OBJS) $(USER_OBJS) $(LIBS) + @echo 'Finished building target: $@' + @echo ' ' + +--- Augustus-3.3.3/auxprogs/utrrnaseq/Debug/src/subdir.mk.orig 2020-04-22 23:13:01.747305000 +0200 ++++ Augustus-3.3.3/auxprogs/utrrnaseq/Debug/src/subdir.mk 2020-04-22 23:13:07.139766000 +0200 +@@ -38,7 +38,7 @@ + src/%.o: ../src/%.cpp + @echo 'Building file: $<' + @echo 'Invoking: GCC C++ Compiler' +- g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@)" -o "$@" "$<" ++ $(CXX) $(CXXFLAGS) -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@)" -o "$@" "$<" + @echo 'Finished building: $<' + @echo ' ' + From 2b97d0a80f1cf4bedeb58919ed143ff5d8c8a174 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 23 Apr 2020 02:07:08 +0200 Subject: [PATCH 155/431] adding easyconfigs: libgit2-1.0.0-GCCcore-8.3.0.eb --- .../l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..1c1f55da4ae --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.0.0' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['6a1fa16a7f6335ce8b2630fbdbb5e57c4027929ebc56fcd1ac55edb141b409b4'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), +] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' From 295f4312305cf847b4f9228c7ed269c99aaa0625 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Wed, 22 Apr 2020 22:58:08 -0500 Subject: [PATCH 156/431] Adjust root_numpy depeendence back to numpy 1.15.0 (depends on PR #10377). --- .../Cython-0.29.16-foss-2018b-Python-3.6.6.eb | 41 +++++++++++++ .../g/GSL/GSL-2.5-GCCcore-7.3.0.eb | 25 ++++++++ .../numpy-1.15.0-foss-2018b-Python-3.6.6.eb | 27 +++++++++ .../ROOT-6.14.06-foss-2018b-Python-3.6.6.eb | 58 +++++++++++++++++++ ...oot_numpy-4.8.0-foss-2018b-Python-3.6.6.eb | 20 +------ 5 files changed, 153 insertions(+), 18 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c88e9ba17d6 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: Apache +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.29.16' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for +the Python language as easy as Python itself. Cython is a source code +translator based on the well-known Pyrex, but supports more cutting +edge functionality and optimizations.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['232755284f942cbb3b43a06cd85974ef3c970a021aef19b5243c03ee2b08fa05'] + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True # Required with "use_pip" + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' \ No newline at end of file diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..8e5316667b7 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.5' + +homepage = 'http://www.gnu.org/software/gsl/' + +description = """ + The GNU Scientific Library (GSL) is a numerical library for C and C++ + programmers. The library provides a wide range of mathematical routines + such as random number generators, special functions and least-squares fitting. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d'] + +builddependencies = [ + ('binutils', '2.30'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..42cbfa6e2c7 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +name = 'numpy' +version = '1.15.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'] + +builddependencies = [ + ('Cython', '0.29.16', versionsuffix), +] + +dependencies = [ + ('Python', '3.6.6'), + ('pytest', '3.8.2', versionsuffix), # Older version used elsehwere +] + +moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c9c9ef4c30a --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,58 @@ +# Why does specifying the easyblock break the build? +# easyblock = 'CMakeMake' + +name = 'ROOT' +version = '6.14.06' +versionsuffix = '-Python-%(pyver)s' + +moduleclass = 'data' + +parallel = 1 # TEMPORARY: Single-thread the build for a clean log file + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +patches = ['ROOT-%(version)s_fix-VDT-target.patch'] +checksums = [ + '0fb943b61396f282b289e35c455a9ab60126229be1bd3f04a8f00b37c13ab432', # root_v6.14.06.source.tar.gz + 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch +] + +builddependencies = [ + ('CMake', '3.12.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('GSL', '2.5'), + ('libxml2', '2.9.8'), + ('PCRE', '8.41'), + ('CFITSIO', '3.45'), + ('freetype', '2.9.1'), + ('Python', '3.6.6'), + ('zlib', '1.2.11'), + ('X11', '20180604'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('GL2PS', '1.4.0'), + ('FFTW', '3.3.8'), + ('SQLite', '3.24.0'), + ('XZ', '5.2.4'), + ('libpng', '1.6.34'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpython=ON -Dpython3=ON -Dpcre=ON -Dzlib=ON" +configopts += " -Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' \ No newline at end of file diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb index f2c2fb59b3b..6246816142e 100644 --- a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -1,16 +1,3 @@ -## -# This is a contribution from Texas A&M University, Mitchell Institute for -# Fundamental Physics and Astronomy -# -# Homepage:: http://mitchell.tamu.edu/ -# -# Copyright:: Copyright 2020 Texas A&M University -# Author:: Michael Kelsey -# License:: CC BY-SA 4.0 -# -# Notes:: -## - easyblock = 'PythonPackage' name = 'root_numpy' @@ -18,10 +5,7 @@ version = '4.8.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://scikit-hep.org/root_numpy/' -description = """root_numpy is a Python extension module that provides -an efficient interface between ROOT and NumPy. root_numpy’s internals -are compiled C++ and can therefore handle large amounts of data much -faster than equivalent pure Python implementations.""" +description = """root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy’s internals are compiled C++ and can therefore handle large amounts of data much faster than equivalent pure Python implementations.""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -34,7 +18,7 @@ checksums = [ dependencies = [ ('Python', '3.6.6'), ('ROOT', '6.14.06', versionsuffix), - ('numpy', '1.18.2', versionsuffix), + ('numpy', '1.15.0', versionsuffix), ] moduleclass = 'math' From 1290f9492ccd891d686c8e03ad6c8983439ee517 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Wed, 22 Apr 2020 22:19:12 -0700 Subject: [PATCH 157/431] Delete ROOT-6.14.06-foss-2018b-Python-3.6.6.eb I don't know why this file was pulled in by `eb --update-pr`, but it's not the correct version. --- .../ROOT-6.14.06-foss-2018b-Python-3.6.6.eb | 58 ------------------- 1 file changed, 58 deletions(-) delete mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index c9c9ef4c30a..00000000000 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,58 +0,0 @@ -# Why does specifying the easyblock break the build? -# easyblock = 'CMakeMake' - -name = 'ROOT' -version = '6.14.06' -versionsuffix = '-Python-%(pyver)s' - -moduleclass = 'data' - -parallel = 1 # TEMPORARY: Single-thread the build for a clean log file - -homepage = 'http://root.cern.ch/drupal/' -description = """The ROOT system provides a set of OO frameworks with all the functionality - needed to handle and analyze large amounts of data in a very efficient way.""" - -toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'pic': True} - -source_urls = ['https://root.cern.ch/download/'] -sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -patches = ['ROOT-%(version)s_fix-VDT-target.patch'] -checksums = [ - '0fb943b61396f282b289e35c455a9ab60126229be1bd3f04a8f00b37c13ab432', # root_v6.14.06.source.tar.gz - 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch -] - -builddependencies = [ - ('CMake', '3.12.1'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('GSL', '2.5'), - ('libxml2', '2.9.8'), - ('PCRE', '8.41'), - ('CFITSIO', '3.45'), - ('freetype', '2.9.1'), - ('Python', '3.6.6'), - ('zlib', '1.2.11'), - ('X11', '20180604'), - ('Mesa', '18.1.1'), - ('libGLU', '9.0.0'), - ('GL2PS', '1.4.0'), - ('FFTW', '3.3.8'), - ('SQLite', '3.24.0'), - ('XZ', '5.2.4'), - ('libpng', '1.6.34'), -] - -# NOTE: Ensure that each configopts string begins with a blank -# disable some components -configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" - -# make sure some components are enabled -configopts += " -Dpython=ON -Dpython3=ON -Dpcre=ON -Dzlib=ON" -configopts += " -Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " - -# Add component-specific settings based on dependencies -configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' \ No newline at end of file From d690bd536021c2977ac6546508bed16d2412c0ea Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 23 Apr 2020 00:30:21 -0500 Subject: [PATCH 158/431] Restore correct version of ROOT-6.14.06...Python-3.6.6.eb; needed by root_numpy. --- .../ROOT-6.14.06-foss-2018b-Python-3.6.6.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..682ba36fe1d --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,53 @@ +name = 'ROOT' +version = '6.14.06' +versionsuffix = '-Python-%(pyver)s' + +moduleclass = 'data' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +patches = ['ROOT-%(version)s_fix-VDT-target.patch'] +checksums = [ + '0fb943b61396f282b289e35c455a9ab60126229be1bd3f04a8f00b37c13ab432', # root_v6.14.06.source.tar.gz + 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch +] + +builddependencies = [ + ('CMake', '3.12.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('GSL', '2.5'), + ('libxml2', '2.9.8'), + ('PCRE', '8.41'), + ('CFITSIO', '3.45'), + ('freetype', '2.9.1'), + ('Python', '3.6.6'), + ('zlib', '1.2.11'), + ('X11', '20180604'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('GL2PS', '1.4.0'), + ('FFTW', '3.3.8'), + ('SQLite', '3.24.0'), + ('XZ', '5.2.4'), + ('libpng', '1.6.34'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpython=ON -Dpython3=ON -Dpcre=ON -Dzlib=ON" +configopts += " -Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' From 429d1a02128812eaaeb132961845f06956286603 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 23 Apr 2020 00:34:26 -0500 Subject: [PATCH 159/431] Attempting to resolve conflicts against easybuilders:develop, only reported on push. --- .../r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb index 682ba36fe1d..5aafcddd6a6 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.14.06-foss-2018b-Python-3.6.6.eb @@ -2,9 +2,7 @@ name = 'ROOT' version = '6.14.06' versionsuffix = '-Python-%(pyver)s' -moduleclass = 'data' - -homepage = 'http://root.cern.ch/drupal/' +homepage = 'https://root.cern.ch/drupal/' description = """The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.""" @@ -51,3 +49,5 @@ configopts += " -Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=O # Add component-specific settings based on dependencies configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +moduleclass = 'data' From 7cdf5566ba43d7dc5c4493cf7993af6a4bacc46a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 08:55:04 +0200 Subject: [PATCH 160/431] adding easyconfigs: CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb --- .../CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..854f8a57c6c --- /dev/null +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,26 @@ +name = 'CPLEX' +version = '12.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.ibm.com/analytics/cplex-optimizer' +description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables + analytical decision support for improving efficiency, + reducing costs, and increasing profitability.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +# the Academic Initiative version (as used in this file) can be downloaded as described on +# https://www.ibm.com/developerworks/community/blogs/jfp/entry/cplex_studio_in_ibm_academic_initiative?lang=en +# a restricted "Community edition" version can be found on +# https://www-01.ibm.com/software/websphere/products/optimization/cplex-studio-community-edition/ +sources = ['cplex_studio%s.linux-x86-64.bin' % ''.join(version.split('.'))] +checksums = ['cd530eb9c6d446bd18b5dc5a3d61070bfad92c3efd6565d2d8e31a2acfb496f7'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Java', '1.8', '', True), + ('Python', '3.7.4'), +] + +moduleclass = 'math' From 63708a81a6ac6fbea4e1f0ba676c365093a3df75 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 10:40:16 +0200 Subject: [PATCH 161/431] update extensions in Python 3.8.2 easyconfig --- .../p/Python/Python-3.8.2-GCCcore-9.3.0.eb | 94 +++++++++---------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb index d59cda2a045..a1d9ddea2d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb @@ -43,7 +43,7 @@ exts_default_options = { } # order is important! -# package versions updated Feb 22nd 2020 +# package versions updated 23 April 2020 exts_list = [ ('pip', '20.0.2', { 'use_pip': False, @@ -65,11 +65,11 @@ exts_list = [ ('paycheck', '1.0.2', { 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), - ('pbr', '5.4.4', { - 'checksums': ['139d2625547dbfa5fb0b81daebb39601c478c21956dc57e2e07b74450a8c506b'], + ('pbr', '5.4.5', { + 'checksums': ['07f558fece33b05caf857474a366dfcc00562bca13dd8b47b2b3e22d9f9bf55c'], }), - ('Cython', '0.29.15', { - 'checksums': ['60d859e1efa5cc80436d58aecd3718ff2e74b987db0518376046adedba97ac30'], + ('Cython', '0.29.16', { + 'checksums': ['232755284f942cbb3b43a06cd85974ef3c970a021aef19b5243c03ee2b08fa05'], }), ('six', '1.14.0', { 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], @@ -84,8 +84,8 @@ exts_list = [ 'modulename': 'dateutil', 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], }), - ('decorator', '4.4.1', { - 'checksums': ['54c38050039232e1db4ad7375cfce6748d7b41c29e95a081c8a6d2c30364a2ce'], + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], }), ('liac-arff', '2.4.0', { 'modulename': 'arff', @@ -107,14 +107,14 @@ exts_list = [ ('idna', '2.9', { 'checksums': ['7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb'], }), - ('pycparser', '2.19', { - 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], }), ('cffi', '1.14.0', { 'checksums': ['2d384f4a127a15ba701207f7639d94106693b6cd64173d6c8988e2c25f3ac2b6'], }), - ('cryptography', '2.8', { - 'checksums': ['3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651'], + ('cryptography', '2.9.2', { + 'checksums': ['a0c30272fb4ddda5f5ffc1089d7405b7a71b0b0f51993cb4e5dbb4590b2fc229'], }), ('pyasn1', '0.4.8', { 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], @@ -129,8 +129,8 @@ exts_list = [ ('paramiko', '2.7.1', { 'checksums': ['920492895db8013f6cc0179293147f830b8c7b21fdfc839b6bad760c27459d9f'], }), - ('pyparsing', '2.4.6', { - 'checksums': ['4c830582a84fb022400b85429791bc551f1f4871c33f23e44f353119e92f969f'], + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], }), ('netifaces', '0.10.9', { 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], @@ -157,8 +157,8 @@ exts_list = [ ('filelock', '3.0.12', { 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], }), - ('virtualenv', '20.0.5', { - 'checksums': ['531b142e300d405bb9faedad4adbeb82b4098b918e35209af2adef3129274aae'], + ('virtualenv', '20.0.18', { + 'checksums': ['ac53ade75ca189bc97b6c1d9ec0f1a50efe33cbf178ae09452dcd9fd309013c1'], }), ('docopt', '0.6.2', { 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], @@ -169,11 +169,11 @@ exts_list = [ ('chardet', '3.0.4', { 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), - ('certifi', '2019.11.28', { - 'checksums': ['25b64c7da4cd7479594d035c08c2d809eb4aab3a26e5a990ea98cc450c320f1f'], + ('certifi', '2020.4.5.1', { + 'checksums': ['51fcb31174be6e6664c5f69e3e1691a2d72a1a12e90f872cbdb1567eb47b6519'], }), - ('urllib3', '1.25.8', { - 'checksums': ['87716c2d2a7121198ebcb7ce7cccf6ce5e9ba539041cfbaeecfb641dc0bf6acc'], + ('urllib3', '1.25.9', { + 'checksums': ['3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527'], }), ('requests', '2.23.0', { 'checksums': ['b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6'], @@ -184,11 +184,11 @@ exts_list = [ ('py_expression_eval', '0.3.9', { 'checksums': ['d80a948f91f78d08f789b0a7c3fb2bd9a34ad625f5ce88c262a6c91189a4abb9'], }), - ('tabulate', '0.8.6', { - 'checksums': ['5470cc6687a091c7042cee89b2946d9235fe9f6d49c193a4ae2ac7bf386737c8'], + ('tabulate', '0.8.7', { + 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], }), - ('ujson', '1.35', { - 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + ('ujson', '2.0.3', { + 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], }), ('atomicwrites', '1.3.0', { 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], @@ -205,8 +205,8 @@ exts_list = [ ('zipp', '1.2.0', { 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], }), - ('importlib_metadata', '1.5.0', { - 'checksums': ['06f5b3a99029c7134207dd882428a66992a9de2bef7c2b699b5641f9886c3302'], + ('importlib_metadata', '1.6.0', { + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], }), ('pluggy', '0.13.1', { 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], @@ -218,24 +218,24 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], }), - ('wcwidth', '0.1.8', { - 'checksums': ['f28b3e8a6483e5d49e7f8949ac1a78314e740333ae305b4ba5defd3e74fb37a8'], + ('wcwidth', '0.1.9', { + 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], }), - ('pytest', '5.3.5', { - 'checksums': ['0d5fe9189a148acc3c3eb2ac8e1ac0742cb7618c084f3d228baaec0c254b318d'], + ('pytest', '5.4.1', { + 'checksums': ['84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970'], }), ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), - ('Jinja2', '2.11.1', { - 'checksums': ['93187ffbc7808079673ef52771baa950426fd664d3aad1d0fa3e95644360e250'], + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], }), - ('packaging', '20.1', { - 'checksums': ['e665345f9eef0c621aa0bf2f8d78cf6d21904eef16a93f020240b704a57f1334'], + ('packaging', '20.3', { + 'checksums': ['3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3'], }), - ('sphinxcontrib-websupport', '1.2.0', { + ('sphinxcontrib-websupport', '1.2.1', { 'modulename': 'sphinxcontrib.websupport', - 'checksums': ['bad3fbd312bc36a31841e06e7617471587ef642bdacdbdddaa8cc30cf251b5ea'], + 'checksums': ['545f5da4bd7757e82b8a23ce3af9500c6ffeedbcb13429fca436ad1e80bd10cf'], }), ('Pygments', '2.5.2', { 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], @@ -255,13 +255,13 @@ exts_list = [ ('alabaster', '0.7.12', { 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), - ('sphinxcontrib-applehelp', '1.0.1', { + ('sphinxcontrib-applehelp', '1.0.2', { 'modulename': 'sphinxcontrib.applehelp', - 'checksums': ['edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897'], + 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], }), - ('sphinxcontrib-devhelp', '1.0.1', { + ('sphinxcontrib-devhelp', '1.0.2', { 'modulename': 'sphinxcontrib.devhelp', - 'checksums': ['6c64b077937330a9128a4da74586e8c2130262f014689b4b89e2d08ee7294a34'], + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], }), ('sphinxcontrib-htmlhelp', '1.0.3', { 'modulename': 'sphinxcontrib.htmlhelp', @@ -271,19 +271,19 @@ exts_list = [ 'modulename': 'sphinxcontrib.jsmath', 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], }), - ('sphinxcontrib-qthelp', '1.0.2', { + ('sphinxcontrib-qthelp', '1.0.3', { 'modulename': 'sphinxcontrib.qthelp', - 'checksums': ['79465ce11ae5694ff165becda529a600c754f4bc459778778c7017374d4d406f'], + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], }), - ('sphinxcontrib-serializinghtml', '1.1.3', { + ('sphinxcontrib-serializinghtml', '1.1.4', { 'modulename': 'sphinxcontrib.serializinghtml', - 'checksums': ['c0efb33f8052c04fd7a26c0a07f1678e8512e0faec19f4aa8f2473a8b81d5227'], + 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], }), - ('Sphinx', '2.4.2', { - 'checksums': ['525527074f2e0c2585f68f73c99b4dc257c34bbe308b27f5f8c7a6e20642742f'], + ('Sphinx', '3.0.2', { + 'checksums': ['d7c6e72c6aa229caf96af82f60a0d286a1521d42496c226fe37f5a75dcfe2941'], }), - ('Click', '7.0', { - 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + ('click', '7.1.1', { + 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], }), ('psutil', '5.7.0', { 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], From 0623823f384bfb9902c8c82f13955e8c70995b55 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 23 Apr 2020 10:57:28 +0200 Subject: [PATCH 162/431] Clang 7.0.1 on GCC 7.3.0-2.30 - included LLVM linker --- .../easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb index 3c9effc3622..6be7f60c0c6 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb @@ -28,6 +28,10 @@ sources = [ 'compiler-rt-%(version)s.src.tar.xz', 'polly-%(version)s.src.tar.xz', 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', ] checksums = [ 'a38dfc4db47102ec79dcc2aa61e93722c5f6f06f0a961073bd84b78fb949419b', # llvm-7.0.1.src.tar.xz @@ -35,6 +39,9 @@ checksums = [ '782edfc119ee172f169c91dd79f2c964fb6b248bd9b73523149030ed505bbe18', # compiler-rt-7.0.1.src.tar.xz '1bf146842a09336b9c88d2d76c2d117484e5fad78786821718653d1a9d57fb71', # polly-7.0.1.src.tar.xz 'bf16b78a678da67d68405214ec7ee59d86a15f599855806192a75dcfca9b0d0c', # openmp-7.0.1.src.tar.xz + '8869aab2dd2d8e00d69943352d3166d159d7eae2615f66a684f4a0999fc74031', # lld-7.0.1.src.tar.xz + '020002618b319dc2a8ba1f2cba88b8cc6a209005ed8ad29f9de0c562c6ebb9f1', # libcxx-7.0.1.src.tar.xz + '8168903a157ca7ab8423d3b974eaa497230b1564ceb57260be2bd14412e8ded8', # libcxxabi-7.0.1.src.tar.xz ] dependencies = [ @@ -49,6 +56,10 @@ builddependencies = [ assertions = True usepolly = True +build_lld = True +libcxx = True +enable_rtti = True + skip_all_tests = True moduleclass = 'compiler' From 247f9dbe23f195bf0f08f9f4ee1bdc19de694d3b Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 23 Apr 2020 11:07:49 +0200 Subject: [PATCH 163/431] adding easyconfigs: artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb, rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb, gotree-0.4.0-binary.eb, goalign-0.3.2-binary.eb, IQ-TREE-1.6.12-foss-2018b.eb, Longshot-0.4.1-foss-2018b.eb, MAFFT-7.427-foss-2018b-with-extensions.eb, MUSCLE-3.8.1551-foss-2018b.eb, nodejs-12.16.1-GCCcore-7.3.0.eb, Rust-1.42.0-GCCcore-7.3.0.eb --- ...20.04.13-foss-2018b-Python-3.6.6-medaka.eb | 133 ++++++++++++++++++ .../g/goalign/goalign-0.3.2-binary.eb | 28 ++++ .../g/gotree/gotree-0.4.0-binary.eb | 28 ++++ .../i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb | 34 +++++ .../l/Longshot/Longshot-0.4.1-foss-2018b.eb | 40 ++++++ .../MAFFT-7.427-foss-2018b-with-extensions.eb | 38 +++++ .../m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb | 30 ++++ .../n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb | 44 ++++++ .../r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb | 28 ++++ ...ampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb | 68 +++++++++ 10 files changed, 471 insertions(+) create mode 100644 easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb create mode 100644 easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb create mode 100644 easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb new file mode 100644 index 00000000000..ccea25cd45c --- /dev/null +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb @@ -0,0 +1,133 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'artic-ncov2019' +# commit 4a7461c3cc9865860d69223ba8360df13a248f13 +version = '2020.04.13' + +local_python_versionsuffix = '-Python-%(pyver)s' +versionsuffix = local_python_versionsuffix + '-medaka' + +homepage = "https://github.com/artic-network/artic-ncov2019" +description = """Initial implementation of an ARTIC bioinformatics platform +for nanopore sequencing of nCoV2019 novel coronavirus.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), # pandas, + ('Biopython', '1.72', local_python_versionsuffix), + ('Pysam', '0.15.1', local_python_versionsuffix), + ('BWA', '0.7.17'), + ('Eigen', '3.3.7', '', True), + ('minimap2', '2.13'), + ('SAMtools', '1.9'), + ('MUSCLE', '3.8.1551'), + ('ETE', '3.1.1', local_python_versionsuffix), + ('MAFFT', '7.427', '-with-extensions'), + ('IQ-TREE', '1.6.12'), + ('snakemake', '5.2.4', local_python_versionsuffix), + ('Longshot', '0.4.1'), + ('medaka', '0.11.4', local_python_versionsuffix), + ('python-parasail', '1.1.16', local_python_versionsuffix), + ('PhyML', '3.3.20190321'), + ('nodejs', '12.16.1'), + ('goalign', '0.3.2', '-binary', True), + ('gotree', '0.4.0', '-binary', True), + ('rampart', '1.2.0rc3', local_python_versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('zipp', '1.0.0', { + 'checksums': ['d38fbe01bbf7a3593a32bc35a9c4453c32bc42b98c377f9bff7e9f8da157786c'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('py', '1.8.1', { + 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], + }), + ('wcwidth', '0.1.9', { + 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], + }), + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('importlib-metadata', '1.6.0', { + 'modulename': 'importlib_metadata', + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + }), + ('more-itertools', '8.2.0', { + 'modulename': 'more_itertools', + 'checksums': ['b1ddb932186d8a6ac451e1d95844b382f55e12686d51ca0c68b6f61f2ab7a507'], + }), + ('packaging', '14.5', { + 'checksums': ['363f9193daa14085b8dfeeb2bf64227bcf1dc85c02ae2a5c6018b01f77e46491'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('pytest', '5.4.1', { + 'checksums': ['84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970'], + }), + ('tqdm', '4.45.0', { + 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], + }), + ('fieldbioinformatics', '1.1.0-rc2', { + 'modulename': False, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], + 'checksums': ['7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073'], + }), + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], + }), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/artic-network/artic-ncov2019/archive/'], + 'sources': [{ + 'download_filename': '4a7461c3cc9865860d69223ba8360df13a248f13.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'artic -v', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb new file mode 100644 index 00000000000..dacfab7ed17 --- /dev/null +++ b/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb @@ -0,0 +1,28 @@ +easyblock = 'Binary' + +name = 'goalign' +version = '0.3.2' +versionsuffix = "-binary" + +homepage = 'https://github.com/evolbioinfo/goalign/' +description = "Goalign is a set of command line tools to manipulate multiple alignments." + +toolchain = SYSTEM + +source_urls = ['https://github.com/evolbioinfo/goalign/releases/download/v%(version)s'] +sources = ['goalign_amd64_linux'] +checksums = ['a0453c63b9c299e9d775ec9b3afe9bac33984bf14a8bcfcdbfa784e4879601d0'] + +postinstallcmds = [ + "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", +] +sanity_check_paths = { + 'files': ['%(name)s_amd64_linux'], + 'dirs': [], +} + +sanity_check_commands = [ + 'goalign --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb b/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb new file mode 100644 index 00000000000..d8db557db07 --- /dev/null +++ b/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb @@ -0,0 +1,28 @@ +easyblock = 'Binary' + +name = 'gotree' +version = '0.4.0' +versionsuffix = "-binary" + +homepage = 'https://github.com/evolbioinfo/gotree/' +description = "GoTree is a set of command line tools to manipulate phylogenetic trees." + +toolchain = SYSTEM + +source_urls = ['https://github.com/evolbioinfo/gotree/releases/download/v%(version)s'] +sources = ['gotree_amd64_linux'] +checksums = ['8527cc7082dfc46f03a1a49e02cd07da7cef94112f0b85c43de3416d53dcb188'] + +postinstallcmds = [ + "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", +] +sanity_check_paths = { + 'files': ['%(name)s_amd64_linux'], + 'dirs': [], +} + +sanity_check_commands = [ + 'gotree --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb new file mode 100644 index 00000000000..7a41be58181 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '1.6.12' + +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'foss', 'version': '2018b'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary +# toolchainopts = {'usempi': True} + +github_account = 'Cibiv' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Eigen', '3.3.7', '', True), +] +dependencies = [('zlib', '1.2.11')] + +configopts = [ + '-DIQTREE_FLAGS=omp', + '-DIQTREE_FLAGS=mpi', +] + +sanity_check_paths = { + 'files': ['bin/iqtree', 'bin/iqtree-mpi'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb new file mode 100644 index 00000000000..f44bdff2d02 --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'Binary' + +name = 'Longshot' +version = '0.4.1' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/pjedge/longshot/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['062529eb47fafc2ef4a1a12ea30a565a0df922b310b6fc5705a1605ce4f495f3'] + +builddependencies = [ + ('binutils', '2.30'), + ('Rust', '1.42.0'), + ('Clang', '7.0.1'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +extract_sources = True + +# https://github.com/rust-bio/rust-htslib/issues/112 +install_cmd = "export LIBCLANG_PATH=${EBROOTCLANG}/lib && " +install_cmd += "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb new file mode 100644 index 00000000000..4c69ab01998 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 7.305 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.427' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://mafft.cbrc.jp/alignment/software/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] +checksums = ['068abcbc20965cbfa4e14c138cbfbcd0d311874ac2fdde384a580ac774f40e26'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb new file mode 100644 index 00000000000..fdb6af2845b --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + 'c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e', # muscle_src_3.8.1551.tar.gz + '5c38f93dcb03f769ecea7e21c83671920d0f3a88102ac6e0a51df23c33414766', # MUSCLE-3.8.1551_fix-mk-hardcoding.patch +] + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..a68fc577392 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '12.16.1' # 12.16.1 was LTS on 2020-05-22 +local_libversion = '72' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['4fe8c3454f9bee5bbe72d44aa25cd931859b3037b7a9473081b3b2bd1b465b95'] + +builddependencies = [ + ('binutils', '2.30'), + ('Python', '2.7.15', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +modextrapaths = {'CPATH': 'include/node'} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..6f7bdda2b6b --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.42.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3f51c302b5d --- /dev/null +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,68 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'rampart' +version = '1.2.0rc3' + +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/artic-network/rampart/" +description = "Read Assignment, Mapping, and Phylogenetic Analysis in Real Time." +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('nodejs', '12.16.1'), + ('Python', '3.6.6'), # pandas, + ('Biopython', '1.72', versionsuffix), + ('snakemake', '5.2.4', versionsuffix), + ('minimap2', '2.13'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + }), +] + +# Don't ever try to install unpacked source of nodejs globally! +# Always use 'npm install -g downloaded_file.tar.gz` or you will end up having broken links and installation will fail. +# -d (debug) and --timing can show errors while downloading dependencies +local_install_cmd = "npm install -d --timing --prefix %(installdir)s -g v%(version)s.tar.gz" + +components = [ + (name, version, { + 'easyblock': 'Binary', + 'source_urls': ['https://github.com/artic-network/rampart/archive/'], + 'sources': [{ + 'filename': 'v%(version)s.tar.gz', + # Don't extract downloaded .tar.gz, just copy that to builddir + 'extract_cmd': "cp %s .", + }], + 'checksums': ['c7696257af96618d05607bd015b5393b8c0827cfee10f4562e4adad5a1bd74f4'], + 'install_cmd': local_install_cmd, + }), +] + +sanity_check_paths = { + 'files': ['bin/binlorry', 'bin/porechop'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'rampart --help' +] + +moduleclass = 'bio' From 64b4a8ed50e3abc5f38b33230521a882f70cdb78 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 23 Apr 2020 11:17:48 +0200 Subject: [PATCH 164/431] updated https --- easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb index 6be7f60c0c6..5cbcc2e2ed1 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '7.0.1' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" From 160c350be2d4c1c694fabb567e76e9010b505c92 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 23 Apr 2020 13:58:13 +0200 Subject: [PATCH 165/431] removed not needed dependency --- .../m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb index 75d9f8c3d91..21a4673613d 100644 --- a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb @@ -32,7 +32,6 @@ dependencies = [ ('prodigal', '2.6.3'), ('MinCED', '0.4.2', '-Java-11'), ('Bio-EUtilities', '1.76'), - ('LWP-Protocol-https', '6.07'), ('swissknife', '1.79'), ] From 78cc99ef1a8a7f55b5c973b53025fde5f9e9f54d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 14:02:05 +0200 Subject: [PATCH 166/431] enable use_pip in ETE easyconfig --- .../easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb index 8d2e3a53a51..13ddb2dbbc8 100644 --- a/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb @@ -20,7 +20,7 @@ dependencies = [ ] download_dep_fail = True -#use_pip = True +use_pip = True options = {'modulename': 'ete3'} From 49031141285f8de9e86abf2d4234c4f14d942b3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 14:26:22 +0200 Subject: [PATCH 167/431] enable sanity_pip_check in ETE 3.1.1 easyconfig --- .../easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb index 13ddb2dbbc8..fe7922894c0 100644 --- a/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'vis' From 73ba37af1eb795348ba632e883e27d4398aa8969 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 14:26:42 +0200 Subject: [PATCH 168/431] swtich to system toolchain in tbl2asn easyconfig --- easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb index 461aa3042e9..3b851f606ff 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb @@ -13,7 +13,7 @@ homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' description = """Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/'] sources = [{'download_filename': 'linux64.tbl2asn.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] From 088d19300ebbd19dfee83e8ce56be42cdd0a1dcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 14:30:49 +0200 Subject: [PATCH 169/431] update tbl2asn dep for MitoZ to 20200302 'release' --- .../easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb | 2 +- ...bl2asn-20190117-linux64.eb => tbl2asn-20200302-linux64.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/t/tbl2asn/{tbl2asn-20190117-linux64.eb => tbl2asn-20200302-linux64.eb} (90%) diff --git a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb index 1c4cf8f66a4..d5bfff12153 100644 --- a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('SAMtools', '1.9'), ('Infernal', '1.1.2'), ('ETE', '3.1.1', versionsuffix), - ('tbl2asn', '20190117', '-linux64', True), + ('tbl2asn', '20200302', '-linux64', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20200302-linux64.eb similarity index 90% rename from easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb rename to easybuild/easyconfigs/t/tbl2asn/tbl2asn-20200302-linux64.eb index 3b851f606ff..f4a95bc866c 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20200302-linux64.eb @@ -6,7 +6,7 @@ easyblock = 'CmdCp' name = 'tbl2asn' -version = '20190117' +version = '20200302' versionsuffix = '-linux64' homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' @@ -17,7 +17,7 @@ toolchain = SYSTEM source_urls = ['ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/'] sources = [{'download_filename': 'linux64.tbl2asn.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] -checksums = ['1f41acb9eacd6e0fa78657b17727b8f94d97490617563686d28b3f6c24d39117'] +checksums = ['7cc1119d3cfcbbffdbd4ecf33cef8bbdd44fc5625c72976bee08b1157625377e'] cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] From c7601ebb0e2b24b565a8cb8de2c8d6784cbcd0da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Apr 2020 16:01:32 +0200 Subject: [PATCH 170/431] adding easyconfigs: MDTraj-1.9.3-foss-2019b-Python-3.7.4.eb --- .../MDTraj-1.9.3-foss-2019b-Python-3.7.4.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..7689972c477 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.3-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'MDTraj' +version = '1.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mdtraj/mdtraj/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['15997a9c2bbe8a5148316a30ae420f9c345797a586369ad064b7fca9bd302bb3'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('zlib', '1.2.11'), +] + +download_dep_fail = True +use_pip = True + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' From fc83f7cf0e237f8e743a8635ac780528c76bd3dc Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 23 Apr 2020 16:20:18 +0200 Subject: [PATCH 171/431] minimap2 (foss-2018b and GCC-8.2.0*) include static lib and header --- .../m/minimap2/minimap2-2.13-foss-2018b.eb | 12 +++++++++--- .../m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb | 12 +++++++++--- 2 files changed, 18 insertions(+), 6 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb mode change 100755 => 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb old mode 100755 new mode 100644 index ba514cabb71..8798c2c599d --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Adam Huffman # Big Data Institute, University of Oxford @@ -24,10 +24,16 @@ source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/' sources = ['%(name)s-%(version)s.tar.bz2'] checksums = ['ac1ce248f4a9c8d47397204ada38bb4739fc2c9b81e6c0894e074b5e89deb76c'] -files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] sanity_check_paths = { - 'files': ['bin/%(name)s'], + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb old mode 100755 new mode 100644 index a81062d252f..b29291d7497 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Adam Huffman # Big Data Institute, University of Oxford @@ -24,10 +24,16 @@ source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/' sources = ['%(name)s-%(version)s.tar.bz2'] checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] -files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] sanity_check_paths = { - 'files': ['bin/%(name)s'], + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], 'dirs': [] } From 505d95541c28fa49bd95a6baca12586f2ea6415e Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 23 Apr 2020 10:51:54 -0500 Subject: [PATCH 172/431] Drop unneeded dependent modules; remove explicit numpy dependence from new root_numpy, provided by Python-3.6.6. --- .../Cython-0.29.16-foss-2018b-Python-3.6.6.eb | 41 ------------------- .../numpy-1.15.0-foss-2018b-Python-3.6.6.eb | 27 ------------ ...oot_numpy-4.8.0-foss-2018b-Python-3.6.6.eb | 1 - 3 files changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb delete mode 100644 easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index c88e9ba17d6..00000000000 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.16-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia -# Homepage: https://www.adelaide.edu.au/phoenix/ -# -# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix -# Authors:: Robert Qiao , Exequiel Sepulveda -# License:: Apache -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'Cython' -version = '0.29.16' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/Cython/' -description = """The Cython language makes writing C extensions for -the Python language as easy as Python itself. Cython is a source code -translator based on the well-known Pyrex, but supports more cutting -edge functionality and optimizations.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['232755284f942cbb3b43a06cd85974ef3c970a021aef19b5243c03ee2b08fa05'] - -dependencies = [('Python', '3.6.6')] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True # Required with "use_pip" - -sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lang' \ No newline at end of file diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index 42cbfa6e2c7..00000000000 --- a/easybuild/easyconfigs/n/numpy/numpy-1.15.0-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,27 +0,0 @@ -name = 'numpy' -version = '1.15.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.numpy.org' -description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: - a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran - code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, - NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be - defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_ZIP] -checksums = ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'] - -builddependencies = [ - ('Cython', '0.29.16', versionsuffix), -] - -dependencies = [ - ('Python', '3.6.6'), - ('pytest', '3.8.2', versionsuffix), # Older version used elsehwere -] - -moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb index 6246816142e..cfc8a7c4b21 100644 --- a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -18,7 +18,6 @@ checksums = [ dependencies = [ ('Python', '3.6.6'), ('ROOT', '6.14.06', versionsuffix), - ('numpy', '1.15.0', versionsuffix), ] moduleclass = 'math' From ca999edbae14674ab9d043634ae97da7575a6012 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 23 Apr 2020 19:53:27 +0200 Subject: [PATCH 173/431] Update easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb Co-Authored-By: Alex Domingo --- .../easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb index 1c1f55da4ae..928e668e8fb 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.0.0-GCCcore-8.3.0.eb @@ -18,8 +18,17 @@ checksums = ['6a1fa16a7f6335ce8b2630fbdbb5e57c4027929ebc56fcd1ac55edb141b409b4'] builddependencies = [ ('binutils', '2.32'), ('CMake', '3.15.3'), + ('pkg-config', '0.29.2'), ] +dependencies = [ + ('PCRE', '8.43'), + # OS dependency should be preferred if the os version is more recent than this version + # ('OpenSSL', '1.1.1b'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + sanity_check_paths = { 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], 'dirs': [] From b15b57328b639701bf6673f24cd59af78448ea91 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 23 Apr 2020 13:50:10 -0500 Subject: [PATCH 174/431] Address testing failures in PR #10424: optional flag settings and whitespace. --- .../root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb | 9 ++++++++- .../r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb | 4 ++++ 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb index cfc8a7c4b21..503a90e83b1 100644 --- a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -5,7 +5,10 @@ version = '4.8.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://scikit-hep.org/root_numpy/' -description = """root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy’s internals are compiled C++ and can therefore handle large amounts of data much faster than equivalent pure Python implementations.""" + +description = """root_numpy is a Python extension module that provides an efficient interface between ROOT and + NumPy. root_numpy’s internals are compiled C++ and can therefore handle large amounts of data much faster than + equivalent pure Python implementations.""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -15,6 +18,10 @@ checksums = [ '5842bbcde92133f60a61f56e9f0a875a0dbc2a567cc65a9ac141ecd72e416878', # root_numpy-4.8.0.zip ] +use_pip = True +sanity_pip_check = True + +download_dep_fail = True dependencies = [ ('Python', '3.6.6'), ('ROOT', '6.14.06', versionsuffix), diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb index 39fbf6998fd..d8b8292a363 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb @@ -23,6 +23,10 @@ source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['7d85fc8fc4ff96a833fa593be401aa4836b755757b518d23d4c00d7a105ce27e'] +use_pip = True +sanity_pip_check = True + +download_dep_fail = True dependencies = [ ('Python', '3.6.6'), ('ROOT', '6.14.06', versionsuffix), From 32556357f7ee784df416bf92efe67ecf769ccf66 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 23 Apr 2020 14:16:21 -0500 Subject: [PATCH 175/431] Remove unnecessary GSL-2.5 from PR. --- .../g/GSL/GSL-2.5-GCCcore-7.3.0.eb | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb deleted file mode 100644 index 8e5316667b7..00000000000 --- a/easybuild/easyconfigs/g/GSL/GSL-2.5-GCCcore-7.3.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '2.5' - -homepage = 'http://www.gnu.org/software/gsl/' - -description = """ - The GNU Scientific Library (GSL) is a numerical library for C and C++ - programmers. The library provides a wide range of mathematical routines - such as random number generators, special functions and least-squares fitting. -""" - -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d'] - -builddependencies = [ - ('binutils', '2.30'), -] - -moduleclass = 'numlib' From aa802a5c7c347ffc249342c37e0144da60155bb9 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 23 Apr 2020 15:19:17 -0500 Subject: [PATCH 176/431] Replace http: with https: in root_numpy 'homepage' link. Too bad --check-contrib doesn't report this. --- .../r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb index 503a90e83b1..9b37593ccc4 100644 --- a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'root_numpy' version = '4.8.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://scikit-hep.org/root_numpy/' +homepage = 'https://scikit-hep.org/root_numpy/' description = """root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy’s internals are compiled C++ and can therefore handle large amounts of data much faster than @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = [ - '5842bbcde92133f60a61f56e9f0a875a0dbc2a567cc65a9ac141ecd72e416878', # root_numpy-4.8.0.zip + '5842bbcde92133f60a61f56e9f0a875a0dbc2a567cc65a9ac141ecd72e416878', # root_numpy-4.8.0.tar.gz ] use_pip = True From 9efd3f95fcd4aa20646d391574b1aaad379afae8 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Fri, 24 Apr 2020 17:11:45 +1200 Subject: [PATCH 177/431] Update Salmon-1.2.0-gompi-2019b.eb --- easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb index 98e93d3807c..a074a1a0ba1 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb @@ -42,8 +42,10 @@ dependencies = [ runtest = 'test' sanity_check_paths = { - 'files': ['bin/salmon', 'lib/libsalmon_core.a'], + 'files': ['bin/%(namelower)s'] + ['lib/lib%s.a' % x for x in ['graphdump', 'ntcard', 'salmon_core', 'twopaco']], 'dirs': [], } +sanity_check_commands = ["salmon --help"] + moduleclass = 'bio' From 9fe4d484a4458ca779a39201b524783ec71098f2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 24 Apr 2020 09:53:26 +0200 Subject: [PATCH 178/431] adding easyconfigs: sympy-1.5.1-foss-2019b-Python-3.7.4.eb, MPC-1.1.0-foss-2019b.eb, gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb and patches: sympy-1.5.1_allpython.patch --- .../gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb | 27 +++ .../easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb | 33 ++++ .../sympy-1.5.1-foss-2019b-Python-3.7.4.eb | 41 +++++ .../s/sympy/sympy-1.5.1_allpython.patch | 162 ++++++++++++++++++ 4 files changed, 263 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.5.1_allpython.patch diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..bb990a023c7 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0b1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30b30707c782e4e355c920d1d998751ffc1b2189070a88a482f08c6e35511939'] + +dependencies = [ + ('Python', '3.7.4'), + ('GMP', '6.1.2'), + ('MPFR', '4.0.2'), + ('MPC', '1.1.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb b/easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb new file mode 100644 index 00000000000..3db55bfdb58 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.1.0' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'] + +dependencies = [ + ('GMP', '6.1.2'), + ('MPFR', '4.0.2'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..3de30912703 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_allpython.patch'] +checksums = [ + 'd77901d748287d15281f5ffe5b0fef62dd38f357c2b827c44ff07f35695f4e7e', # sympy-1.5.1.tar.gz + 'f1101b947a682f089cc39ba9bd2045c4b8620c6488134121479cbde425a864ee', # sympy-1.5.1_allpython.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('gmpy2', '2.1.0b1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.5.1_allpython.patch b/easybuild/easyconfigs/s/sympy/sympy-1.5.1_allpython.patch new file mode 100644 index 00000000000..ccf2a14f500 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.5.1_allpython.patch @@ -0,0 +1,162 @@ +Updated patch file sympy-1.3_allpython.patch for version 1.5.1 + added fix for test_debug_output() +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +# this patch contains fixes for two different problems: +# +# *** IOError: [Errno 39] aka "Directory not empty" FIX *** +# +# - 22.1.2019, J. Dvoracek (Institute of Physics | Czech Academy of Sciences, www.fzu.cz +# +# While running test step on NFS share, it fails with: +# File "(...)sympy/utilities/_compilation/tests/test_compilation.py", line 61 +# in test_compile_link_import_strings +# shutil.rmtree(info['build_dir']) +# File "(...)lib/python3.6/shutil.py", line 484, in rmtree +# onerror(os.rmdir, path, sys.exc_info()) +# File "(...)lib/python3.6/shutil.py", line 482, in rmtree +# os.rmdir(path) +# OSError: [Errno 39] Directory not empty: '(...)sympy-1.3/tmp695y36rc' +# +# shmem.rmtree() is called when file inside is stil being used, so files are renamed to .nfsXXXXX +# and rmtee fails with Errno 39 (Directory not empty) error. +# As we're running the tests in Easybuild, we can assume that the buil_dir will be deleted by EasyBuild, +# so we can safely skip the delete operation +# +# *** IOError: [Errno 2] aka "No such file or directory" FIX *** +# +# - original (1.10.2018, B. Hajgato (Free Ubiversity Brussels - VUB) +# +# During some test jobs, an error +# IOError: [Errno 2] No such file or directory: '/tmp/hajgato/link/eb-Tfchx1/tmpx5Z16m/_newton.c' +# occured, if the tmpdir was a symlink or any of its subdir was a symlink. Therefore, realpath is used. +# +# - update (22.1.2019, J. Dvoracek (Institute of Physics | Czech Academy of Sciences, www.fzu.cz ) +# +# fix above deals just with the occurence in Python2. Now we use the same trick for Python3 too. + +--- sympy-1.3/sympy/utilities/_compilation/tests/test_compilation.py_orig 2019-01-21 21:47:46.552355000 +0100 ++++ sympy-1.3/sympy/utilities/_compilation/tests/test_compilation.py 2019-01-21 21:48:16.358586000 +0100 +@@ -58,4 +58,4 @@ + assert numpy.allclose(res_mod, res_npy) + finally: + if info and info['build_dir']: +- shutil.rmtree(info['build_dir']) ++ pass + +diff -ur sympy-1.5.1.orig/sympy/codegen/tests/test_algorithms.py sympy-1.5.1/sympy/codegen/tests/test_algorithms.py +--- sympy-1.5.1.orig/sympy/codegen/tests/test_algorithms.py 2019-12-21 00:38:00.000000000 +0100 ++++ sympy-1.5.1/sympy/codegen/tests/test_algorithms.py 2020-04-20 12:39:50.061465000 +0200 +@@ -11,9 +11,11 @@ + from sympy.external import import_module + from sympy.printing.ccode import ccode + from sympy.utilities._compilation import compile_link_import_strings, has_c, has_fortran +-from sympy.utilities._compilation.util import TemporaryDirectory, may_xfail ++from sympy.utilities._compilation.util import may_xfail ++from sympy.utilities._compilation.util import TemporaryDirectory_DND as TemporaryDirectory + from sympy.utilities.pytest import skip, raises + ++ + cython = import_module('cython') + wurlitzer = import_module('wurlitzer') + +--- sympy-1.3/sympy/codegen/tests/test_fnodes.py.orig 2018-09-06 21:27:20.000000000 +0200 ++++ sympy-1.3/sympy/codegen/tests/test_fnodes.py 2019-01-21 18:44:46.718472000 +0100 +@@ -13,7 +13,8 @@ + from sympy.external import import_module + from sympy.printing.fcode import fcode + from sympy.utilities._compilation import has_fortran, compile_run_strings, compile_link_import_strings +-from sympy.utilities._compilation.util import TemporaryDirectory, may_xfail ++from sympy.utilities._compilation.util import may_xfail ++from sympy.utilities._compilation.util import TemporaryDirectory_DND as TemporaryDirectory + from sympy.utilities.pytest import skip + + cython = import_module('cython') + +--- sympy-1.3/sympy/codegen/tests/test_applications.py.orig 2019-01-21 18:41:24.256877000 +0100 ++++ sympy-1.3/sympy/codegen/tests/test_applications.py 2019-01-21 18:43:57.439442000 +0100 +@@ -3,7 +3,8 @@ + from sympy.external import import_module + from sympy.printing.ccode import ccode + from sympy.utilities._compilation import compile_link_import_strings, has_c +-from sympy.utilities._compilation.util import TemporaryDirectory, may_xfail ++from sympy.utilities._compilation.util import TemporaryDirectory_DND as TemporaryDirectory ++from sympy.utilities._compilation.util import may_xfail + from sympy.utilities.pytest import skip + from sympy.sets import Range + from sympy.codegen.ast import ( + +--- sympy-1.3/sympy/utilities/_compilation/compilation.py.orig 2019-01-21 17:28:36.327899000 +0100 ++++ sympy-1.3/sympy/utilities/_compilation/compilation.py 2019-01-21 17:31:32.197254000 +0100 +@@ -535,7 +535,8 @@ + return mod + + def _write_sources_to_build_dir(sources, build_dir): +- build_dir = build_dir or tempfile.mkdtemp() ++ #build_dir = build_dir or tempfile.mkdtemp() ++ build_dir = build_dir or tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix())) + if not os.path.isdir(build_dir): + raise OSError("Non-existent directory: ", build_dir) + +--- sympy-1.3/sympy/utilities/_compilation/util.py.orig 2018-09-06 21:27:21.000000000 +0200 ++++ sympy-1.3/sympy/utilities/_compilation/util.py 2019-01-21 20:19:25.030436000 +0100 +@@ -25,21 +25,26 @@ + return func + + +-if sys.version_info[0] == 2: +- class FileNotFoundError(IOError): +- pass ++class FileNotFoundError(IOError): ++ pass + +- class TemporaryDirectory(object): +- def __init__(self): +- self.path = tempfile.mkdtemp() +- def __enter__(self): +- return self.path +- def __exit__(self, exc, value, tb): +- shutil.rmtree(self.path) +-else: +- FileNotFoundError = FileNotFoundError +- TemporaryDirectory = tempfile.TemporaryDirectory ++class TemporaryDirectory(object): ++ def __init__(self): ++ # self.path = tempfile.mkdtemp() ++ self.path = tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix())) ++ def __enter__(self): ++ return self.path ++ def __exit__(self, exc, value, tb): ++ shutil.rmtree(self.path) + ++class TemporaryDirectory_DND(object): ++ def __init__(self): ++ # self.path = tempfile.mkdtemp() ++ self.path = tempfile.mkdtemp(prefix=os.path.realpath(tempfile.gettempprefix())) ++ def __enter__(self): ++ return self.path ++ def __exit__(self, exc, value, tb): ++ pass + + class CompilerNotFoundError(FileNotFoundError): + pass +diff -ur sympy-1.5.1.orig/sympy/utilities/tests/test_misc.py sympy-1.5.1/sympy/utilities/tests/test_misc.py +--- sympy-1.5.1.orig/sympy/utilities/tests/test_misc.py 2019-12-21 00:38:01.000000000 +0100 ++++ sympy-1.5.1/sympy/utilities/tests/test_misc.py 2020-04-23 12:51:25.097893000 +0200 +@@ -3,6 +3,7 @@ + from sympy.utilities.misc import translate, replace, ordinal, rawlines, strlines + import sys + from subprocess import Popen, PIPE ++import os + + def test_translate(): + abc = 'abc' +@@ -108,6 +109,10 @@ + + def test_debug_output(): + env = {'SYMPY_DEBUG':'True'} ++ env.update({ ++ 'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH', ''), ++ 'PYTHONPATH': os.environ.get('PYTHONPATH', ''), ++ }) + cmd = 'from sympy import *; x = Symbol("x"); print(integrate((1-cos(x))/x, x))' + cmdline = [sys.executable, '-c', cmd] + proc = Popen(cmdline, env=env, stdout=PIPE, stderr=PIPE) From effdd075a5a665aec93890b2f42f834849cc2a2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2020 10:08:23 +0200 Subject: [PATCH 179/431] avoid double - in versionsuffix of torchtext --- ...orchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/t/torchtext/{torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0--Python-3.7.4.eb => torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb} (91%) diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0--Python-3.7.4.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb similarity index 91% rename from easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0--Python-3.7.4.eb rename to easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb index 2210d2efd84..8b5ea20b4ca 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0--Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.5.0-fosscuda-2019b-PyTorch-1.4.0-Python-3.7.4.eb @@ -4,7 +4,7 @@ name = 'torchtext' version = '0.5.0' local_pytorchver = '1.4.0' local_pyversuff = '-Python-%(pyver)s' -versionsuffix = '-PyTorch-%s-%s' % (local_pytorchver, local_pyversuff) +versionsuffix = '-PyTorch-%s%s' % (local_pytorchver, local_pyversuff) homepage = 'https://github.com/pytorch/text' description = "Data loaders and abstractions for text and NLP" From 1e88925aa43ead0d174dcb081c410932e6299796 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 24 Apr 2020 10:43:30 +0200 Subject: [PATCH 180/431] adding easyconfigs: goalign-0.3.2.eb, gotree-0.4.0.eb and patches: goalign-0.3.2_go-mod.patch, gotree-0.4.0_go-mod.patch --- .../easyconfigs/g/goalign/goalign-0.3.2.eb | 34 +++ .../g/goalign/goalign-0.3.2_go-mod.patch | 202 ++++++++++++++++ .../easyconfigs/g/gotree/gotree-0.4.0.eb | 34 +++ .../g/gotree/gotree-0.4.0_go-mod.patch | 224 ++++++++++++++++++ 4 files changed, 494 insertions(+) create mode 100644 easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb create mode 100644 easybuild/easyconfigs/g/goalign/goalign-0.3.2_go-mod.patch create mode 100644 easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb create mode 100644 easybuild/easyconfigs/g/gotree/gotree-0.4.0_go-mod.patch diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb new file mode 100644 index 00000000000..49597f83d08 --- /dev/null +++ b/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'goalign' +version = '0.3.2' + +homepage = 'https://github.com/evolbioinfo/goalign' +description = """Goalign is a set of command line tools to manipulate multiple alignments.""" + +toolchain = SYSTEM + +# https://github.com/evolbioinfo/goalign +github_account = 'evolbioinfo' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [('%(name)s-%(version)s_go-mod.patch', 1)] +checksums = [ + 'e499889916eaaa6955f179e45870b06e862c6a90c6fc2a7d62d618e965e26c01', # v0.3.2.tar.gz + 'e055d77d901f4bc13cf32d010b2b44e28c07a764778dd0e8d752b482ed26165f', # goalign-0.3.2_go-mod.patch +] + +builddependencies = [ + ('Go', '1.14'), +] + +sanity_check_paths = { + 'files': ['bin/goalign'], + 'dirs': [], +} + +sanity_check_commands = [ + 'goalign --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2_go-mod.patch b/easybuild/easyconfigs/g/goalign/goalign-0.3.2_go-mod.patch new file mode 100644 index 00000000000..71f2ecb5cd3 --- /dev/null +++ b/easybuild/easyconfigs/g/goalign/goalign-0.3.2_go-mod.patch @@ -0,0 +1,202 @@ +Add go.mod and go.sum to have reproducible build +# Generated by GoPackge Easyblock +# modulename = 'github.com/evolbioinfo/goalign' + +author: Pavel Grochal (INUITS) +diff -ru --new-file goalign-0.3.2.orig/go.mod goalign-0.3.2/go.mod +--- goalign-0.3.2.orig/go.mod 1970-01-01 01:00:00.000000000 +0100 ++++ goalign-0.3.2/go.mod 2020-04-23 17:52:16.032124296 +0200 +@@ -0,0 +1,16 @@ ++module github.com/evolbioinfo/goalign ++ ++go 1.14 ++ ++require ( ++ github.com/abiosoft/ishell v2.0.0+incompatible // indirect ++ github.com/abiosoft/readline v0.0.0-20180607040430-155bce2042db // indirect ++ github.com/armon/go-radix v1.0.0 ++ github.com/chzyer/logex v1.1.10 // indirect ++ github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1 // indirect ++ github.com/fatih/color v1.9.0 // indirect ++ github.com/flynn-archive/go-shlex v0.0.0-20150515145356-3f9db97f8568 // indirect ++ github.com/fredericlemoine/cobrashell v0.0.0-20180921081141-49c72f93426c ++ github.com/spf13/cobra v1.0.0 ++ gonum.org/v1/gonum v0.7.0 ++) +diff -ru --new-file goalign-0.3.2.orig/go.sum goalign-0.3.2/go.sum +--- goalign-0.3.2.orig/go.sum 1970-01-01 01:00:00.000000000 +0100 ++++ goalign-0.3.2/go.sum 2020-04-23 17:54:44.277063543 +0200 +@@ -0,0 +1,173 @@ ++cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= ++github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= ++github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU= ++github.com/abiosoft/ishell v2.0.0+incompatible h1:zpwIuEHc37EzrsIYah3cpevrIc8Oma7oZPxr03tlmmw= ++github.com/abiosoft/ishell v2.0.0+incompatible/go.mod h1:HQR9AqF2R3P4XXpMpI0NAzgHf/aS6+zVXRj14cVk9qg= ++github.com/abiosoft/readline v0.0.0-20180607040430-155bce2042db h1:CjPUSXOiYptLbTdr1RceuZgSFDQ7U15ITERUGrUORx8= ++github.com/abiosoft/readline v0.0.0-20180607040430-155bce2042db/go.mod h1:rB3B4rKii8V21ydCbIzH5hZiCQE7f5E9SzUb/ZZx530= ++github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw= ++github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc= ++github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= ++github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8= ++github.com/armon/go-radix v1.0.0 h1:F4z6KzEeeQIMeLFa97iZU6vupzoecKdU5TX24SNppXI= ++github.com/armon/go-radix v1.0.0/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8= ++github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q= ++github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8= ++github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc= ++github.com/chzyer/logex v1.1.10 h1:Swpa1K6QvQznwJRcfTfQJmTE72DqScAa40E+fbHEXEE= ++github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI= ++github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1 h1:q763qf9huN11kDQavWsoZXJNW3xEE4JJyHa5Q25/sd8= ++github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU= ++github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= ++github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk= ++github.com/coreos/etcd v3.3.10+incompatible/go.mod h1:uF7uidLiAD3TWHmW31ZFd/JWoc32PjwdhPthX9715RE= ++github.com/coreos/go-semver v0.2.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk= ++github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4= ++github.com/coreos/pkg v0.0.0-20180928190104-399ea9e2e55f/go.mod h1:E3G3o1h8I7cfcXa63jLwjI0eiQQMgzzUDFVpN/nH/eA= ++github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU= ++github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= ++github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= ++github.com/dgrijalva/jwt-go v3.2.0+incompatible/go.mod h1:E3ru+11k8xSBh+hMPgOLZmtrrCbhqsmaPHjLKYnJCaQ= ++github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no= ++github.com/fatih/color v1.9.0 h1:8xPHl4/q1VyqGIPif1F+1V3Y3lSmrq01EabUW3CoW5s= ++github.com/fatih/color v1.9.0/go.mod h1:eQcE1qtQxscV5RaZvpXrrb8Drkc3/DdQ+uUYCNjL+zU= ++github.com/flynn-archive/go-shlex v0.0.0-20150515145356-3f9db97f8568 h1:BMXYYRWTLOJKlh+lOBt6nUQgXAfB7oVIQt5cNreqSLI= ++github.com/flynn-archive/go-shlex v0.0.0-20150515145356-3f9db97f8568/go.mod h1:rZfgFAXFS/z/lEd6LJmf9HVZ1LkgYiHx5pHhV5DR16M= ++github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k= ++github.com/fredericlemoine/cobrashell v0.0.0-20180921081141-49c72f93426c h1:SSzQJSqpN76VmjR4bg6oouUJAXfd6Vgw8wKun3gBNPo= ++github.com/fredericlemoine/cobrashell v0.0.0-20180921081141-49c72f93426c/go.mod h1:aFIc1y3MUNi6cxWYSJsSoV8ZIdRMaM8W6KWH4wV8k1k= ++github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo= ++github.com/ghodss/yaml v1.0.0/go.mod h1:4dBDuWmgqj2HViK6kFavaiC9ZROes6MMH2rRYeMEF04= ++github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2as= ++github.com/go-logfmt/logfmt v0.3.0/go.mod h1:Qt1PoO58o5twSAckw1HlFXLmHsOX5/0LbT9GBnD5lWE= ++github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V4qmtdjCk= ++github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY= ++github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ= ++github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4= ++github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k= ++github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q= ++github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= ++github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= ++github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= ++github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= ++github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ= ++github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M= ++github.com/gorilla/websocket v1.4.0/go.mod h1:E7qHFY5m1UJ88s3WnNqhKjPHQ0heANvMoAMk2YaljkQ= ++github.com/grpc-ecosystem/go-grpc-middleware v1.0.0/go.mod h1:FiyG127CGDf3tlThmgyCl78X/SZQqEOJBCDaAfeWzPs= ++github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0/go.mod h1:8NvIoxWQoOIhqOTXgfV/d3M/q6VIi02HzZEHgUlZvzk= ++github.com/grpc-ecosystem/grpc-gateway v1.9.0/go.mod h1:vNeuVxBJEsws4ogUvrchl83t/GYV9WGTSLVdBhOQFDY= ++github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ= ++github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM= ++github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= ++github.com/jonboulle/clockwork v0.1.0/go.mod h1:Ii8DK3G1RaLaWxj9trq07+26W01tbo22gdxWY5EU2bo= ++github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w= ++github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes= ++github.com/kisielk/errcheck v1.1.0/go.mod h1:EZBBE59ingxPouuu3KfxchcWSUPOHkagtvWXihfKN4Q= ++github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck= ++github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ= ++github.com/kr/logfmt v0.0.0-20140226030751-b84e30acd515/go.mod h1:+0opPa2QZZtGFBFZlji/RkVcI2GknAs/DXo4wKdlNEc= ++github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo= ++github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ= ++github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI= ++github.com/magiconair/properties v1.8.0/go.mod h1:PppfXfuXeibc/6YijjN8zIbojt8czPbwD3XqdrwzmxQ= ++github.com/mattn/go-colorable v0.1.4 h1:snbPLB8fVfU9iwbbo30TPtbLRzwWu6aJS6Xh4eaaviA= ++github.com/mattn/go-colorable v0.1.4/go.mod h1:U0ppj6V5qS13XJ6of8GYAs25YV2eR4EVcfRqFIhoBtE= ++github.com/mattn/go-isatty v0.0.8/go.mod h1:Iq45c/XA43vh69/j3iqttzPXn0bhXyGjM0Hdxcsrc5s= ++github.com/mattn/go-isatty v0.0.11 h1:FxPOTFNqGkuDUGi3H/qkUbQO4ZiBa2brKq5r0l8TGeM= ++github.com/mattn/go-isatty v0.0.11/go.mod h1:PhnuNfih5lzO57/f3n+odYbM4JtupLOxQOAqxQCu2WE= ++github.com/matttproud/golang_protobuf_extensions v1.0.1/go.mod h1:D8He9yQNgCq6Z5Ld7szi9bcBfOoFv/3dc6xSMkL2PC0= ++github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= ++github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y= ++github.com/mwitkow/go-conntrack v0.0.0-20161129095857-cc309e4a2223/go.mod h1:qRWi+5nqEBWmkhHvq77mSJWrCKwh8bxhgT7d/eI7P4U= ++github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn4U= ++github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic= ++github.com/pkg/errors v0.8.0/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= ++github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM= ++github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4= ++github.com/prometheus/client_golang v0.9.1/go.mod h1:7SWBe2y4D6OKWSNQJUaRYU/AaXPKyh/dDVn+NZz0KFw= ++github.com/prometheus/client_golang v0.9.3/go.mod h1:/TN21ttK/J9q6uSwhBd54HahCDft0ttaMvbicHlPoso= ++github.com/prometheus/client_model v0.0.0-20180712105110-5c3871d89910/go.mod h1:MbSGuTsp3dbXC40dX6PRTWyKYBIrTGTE9sqQNg2J8bo= ++github.com/prometheus/client_model v0.0.0-20190129233127-fd36f4220a90/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA= ++github.com/prometheus/common v0.0.0-20181113130724-41aa239b4cce/go.mod h1:daVV7qP5qjZbuso7PdcryaAu0sAZbrN9i7WWcTMWvro= ++github.com/prometheus/common v0.4.0/go.mod h1:TNfzLD0ON7rHzMJeJkieUDPYmFC7Snx/y86RQel1bk4= ++github.com/prometheus/procfs v0.0.0-20181005140218-185b4288413d/go.mod h1:c3At6R/oaqEKCNdg8wHV1ftS6bRYblBhIjjI8uT2IGk= ++github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084/go.mod h1:TjEm7ze935MbeOT/UhFTIMYKhuLP4wbCsTZCD3I8kEA= ++github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40TwIPHuXU= ++github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg= ++github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= ++github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc= ++github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo= ++github.com/soheilhy/cmux v0.1.4/go.mod h1:IM3LyeVVIOuxMH7sFAkER9+bJ4dT7Ms6E4xg4kGIyLM= ++github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA= ++github.com/spf13/afero v1.1.2/go.mod h1:j4pytiNVoe2o6bmDsKpLACNPDBIoEAkihy7loJ1B0CQ= ++github.com/spf13/cast v1.3.0/go.mod h1:Qx5cxh0v+4UWYiBimWS+eyWzqEqokIECu5etghLkUJE= ++github.com/spf13/cobra v1.0.0 h1:6m/oheQuQ13N9ks4hubMG6BnvwOeaJrqSPLahSnczz8= ++github.com/spf13/cobra v1.0.0/go.mod h1:/6GTrnGXV9HjY+aR4k0oJ5tcvakLuG6EuKReYlHNrgE= ++github.com/spf13/jwalterweatherman v1.0.0/go.mod h1:cQK4TGJAtQXfYWX+Ddv3mKDzgVb68N+wFjFa4jdeBTo= ++github.com/spf13/pflag v1.0.3 h1:zPAT6CGy6wXeQ7NtTnaTerfKOsV6V6F8agHXFiazDkg= ++github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnInEg4= ++github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/yZzE= ++github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= ++github.com/stretchr/testify v1.2.2 h1:bSDNvY7ZPG5RlJ8otE/7V6gMiyenm9RtJ7IUVIAoJ1w= ++github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= ++github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= ++github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= ++github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= ++github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= ++go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU= ++go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= ++go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0= ++go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q= ++golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= ++golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= ++golang.org/x/exp v0.0.0-20180321215751-8460e604b9de/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/exp v0.0.0-20180807140117-3d87b88a115f/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2 h1:y102fOLFqhV41b+4GPiJoa0k/x+pJcEi2/HB1Y5T6fU= ++golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod h1:ux5Hcp/YLpHSI86hEcLt0YII63i6oz57MZXIpbrjZUs= ++golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE= ++golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc= ++golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20181114220301-adae6a3d119a/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20181220203305-927f97764cc3/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= ++golang.org/x/net v0.0.0-20190522155817-f3200d17e092/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks= ++golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U= ++golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181107165924-66b7b1311ac8/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190222072716-a9d3bda3a223/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20191026070338-33540a1f6037 h1:YyJpGZS1sBuBCzLAR1VEpK193GlqGZbnPFnPV/5Rsb4= ++golang.org/x/sys v0.0.0-20191026070338-33540a1f6037/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= ++golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= ++golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20180525024113-a5b4c53f6e8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190206041539-40960b6deb8e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= ++gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod h1:Y+Yx5eoAFn32cQvJDxZx5Dpnq+c3wtXuadVZAcxbbBo= ++gonum.org/v1/gonum v0.7.0 h1:Hdks0L0hgznZLG9nzXb8vZ0rRvqNvAcgAp84y7Mwkgw= ++gonum.org/v1/gonum v0.7.0/go.mod h1:L02bwd0sqlsvRv41G7wGWFCsVNZFv/k1xzGIxeANHGM= ++gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0 h1:OE9mWmgKkjJyEmDAAtGMPjXu+YNeGvK9VTSHY6+Qihc= ++gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0/go.mod h1:wa6Ws7BG/ESfp6dHfk7C6KdzKA7wR7u/rKwOGE66zvw= ++gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod h1:Wt8AAjI+ypCyYX3nZBvf6cAIx93T+c/OS2HFAYskSZc= ++google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= ++google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= ++google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c= ++google.golang.org/grpc v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= ++gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw= ++gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo= ++gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74= ++gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= ++rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4= ++ diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb b/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb new file mode 100644 index 00000000000..2c870f187e7 --- /dev/null +++ b/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'gotree' +version = '0.4.0' + +homepage = 'https://github.com/evolbioinfo/gotree' +description = """GoTree is a set of command line tools to manipulate phylogenetic trees.""" + +toolchain = SYSTEM + +# https://github.com/evolbioinfo/gotree +github_account = 'evolbioinfo' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [('%(name)s-%(version)s_go-mod.patch', 1)] +checksums = [ + '3b7610eb351624b06b2b785ec16fe102120b4f0e2bb3507d1f9f771d720ad050', # v0.4.0.tar.gz + '503d5cf96a0dfdf0bf994c086fb58519ae84cc279fa8d34f5fd7d976dca2fbf8', # gotree-0.4.0_go-mod.patch +] + +builddependencies = [ + ('Go', '1.14'), +] + +sanity_check_paths = { + 'files': ['bin/gotree'], + 'dirs': [], +} + +sanity_check_commands = [ + 'gotree --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0_go-mod.patch b/easybuild/easyconfigs/g/gotree/gotree-0.4.0_go-mod.patch new file mode 100644 index 00000000000..c1000c59610 --- /dev/null +++ b/easybuild/easyconfigs/g/gotree/gotree-0.4.0_go-mod.patch @@ -0,0 +1,224 @@ +Add go.mod and go.sum to have reproducible build +# Generated by GoPackge Easyblock +# modulename = 'github.com/evolbioinfo/gotree' +# forced_deps = [ +# ('github.com/fredericlemoine/gostats', 'e750742f8b05a600f247b0f866a10e41d0a2128c') +# ] + +author: Pavel Grochal (INUITS) +diff -ru --new-file gotree-0.4.0.orig/go.mod gotree-0.4.0/go.mod +--- gotree-0.4.0.orig/go.mod 1970-01-01 01:00:00.000000000 +0100 ++++ gotree-0.4.0/go.mod 2020-04-24 10:07:43.371131509 +0200 +@@ -0,0 +1,24 @@ ++module github.com/evolbioinfo/gotree ++ ++go 1.14 ++ ++require ( ++ github.com/abiosoft/ishell v2.0.0+incompatible // indirect ++ github.com/abiosoft/readline v0.0.0-20180607040430-155bce2042db // indirect ++ github.com/ajstarks/svgo v0.0.0-20200320125537-f189e35d30ca ++ github.com/armon/go-radix v1.0.0 // indirect ++ github.com/chzyer/logex v1.1.10 // indirect ++ github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1 // indirect ++ github.com/evolbioinfo/goalign v0.3.2 ++ github.com/fatih/color v1.9.0 // indirect ++ github.com/flynn-archive/go-shlex v0.0.0-20150515145356-3f9db97f8568 // indirect ++ github.com/fredericlemoine/bitset v1.2.0 ++ github.com/fredericlemoine/cobrashell v0.0.0-20180921081141-49c72f93426c ++ github.com/fredericlemoine/gostats v0.1.1-0.20190718132557-e750742f8b05 ++ github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 ++ github.com/jlaffaye/ftp v0.0.0-20200422224957-b9f3ade29122 ++ github.com/llgcode/draw2d v0.0.0-20200110163050-b96d8208fcfc ++ github.com/spf13/cobra v1.0.0 ++ golang.org/x/image v0.0.0-20200119044424-58c23975cae1 ++) ++ +diff -ru --new-file gotree-0.4.0.orig/go.sum gotree-0.4.0/go.sum +--- gotree-0.4.0.orig/go.sum 1970-01-01 01:00:00.000000000 +0100 ++++ gotree-0.4.0/go.sum 2020-04-24 10:07:41.711124851 +0200 +@@ -0,0 +1,184 @@ ++cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= ++github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= ++github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU= ++github.com/abiosoft/ishell v2.0.0+incompatible h1:zpwIuEHc37EzrsIYah3cpevrIc8Oma7oZPxr03tlmmw= ++github.com/abiosoft/ishell v2.0.0+incompatible/go.mod h1:HQR9AqF2R3P4XXpMpI0NAzgHf/aS6+zVXRj14cVk9qg= ++github.com/abiosoft/readline v0.0.0-20180607040430-155bce2042db h1:CjPUSXOiYptLbTdr1RceuZgSFDQ7U15ITERUGrUORx8= ++github.com/abiosoft/readline v0.0.0-20180607040430-155bce2042db/go.mod h1:rB3B4rKii8V21ydCbIzH5hZiCQE7f5E9SzUb/ZZx530= ++github.com/ajstarks/svgo v0.0.0-20200320125537-f189e35d30ca h1:kWzLcty5V2rzOqJM7Tp/MfSX0RMSI1x4IOLApEefYxA= ++github.com/ajstarks/svgo v0.0.0-20200320125537-f189e35d30ca/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw= ++github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc= ++github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= ++github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8= ++github.com/armon/go-radix v1.0.0 h1:F4z6KzEeeQIMeLFa97iZU6vupzoecKdU5TX24SNppXI= ++github.com/armon/go-radix v1.0.0/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8= ++github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q= ++github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8= ++github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc= ++github.com/chzyer/logex v1.1.10 h1:Swpa1K6QvQznwJRcfTfQJmTE72DqScAa40E+fbHEXEE= ++github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI= ++github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1 h1:q763qf9huN11kDQavWsoZXJNW3xEE4JJyHa5Q25/sd8= ++github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU= ++github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= ++github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk= ++github.com/coreos/etcd v3.3.10+incompatible/go.mod h1:uF7uidLiAD3TWHmW31ZFd/JWoc32PjwdhPthX9715RE= ++github.com/coreos/go-semver v0.2.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk= ++github.com/coreos/go-systemd 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v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg= ++github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= ++github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc= ++github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo= ++github.com/soheilhy/cmux v0.1.4/go.mod h1:IM3LyeVVIOuxMH7sFAkER9+bJ4dT7Ms6E4xg4kGIyLM= ++github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA= ++github.com/spf13/afero v1.1.2/go.mod h1:j4pytiNVoe2o6bmDsKpLACNPDBIoEAkihy7loJ1B0CQ= ++github.com/spf13/cast v1.3.0/go.mod h1:Qx5cxh0v+4UWYiBimWS+eyWzqEqokIECu5etghLkUJE= ++github.com/spf13/cobra v1.0.0 h1:6m/oheQuQ13N9ks4hubMG6BnvwOeaJrqSPLahSnczz8= ++github.com/spf13/cobra v1.0.0/go.mod h1:/6GTrnGXV9HjY+aR4k0oJ5tcvakLuG6EuKReYlHNrgE= ++github.com/spf13/jwalterweatherman v1.0.0/go.mod h1:cQK4TGJAtQXfYWX+Ddv3mKDzgVb68N+wFjFa4jdeBTo= ++github.com/spf13/pflag v1.0.3 h1:zPAT6CGy6wXeQ7NtTnaTerfKOsV6V6F8agHXFiazDkg= ++github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnInEg4= ++github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/yZzE= ++github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= ++github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= ++github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= ++github.com/stretchr/testify v1.4.0 h1:2E4SXV/wtOkTonXsotYi4li6zVWxYlZuYNCXe9XRJyk= ++github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4= ++github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= ++github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= ++github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= ++github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= ++go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU= ++go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= ++go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0= ++go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q= ++golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= ++golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= ++golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod h1:ux5Hcp/YLpHSI86hEcLt0YII63i6oz57MZXIpbrjZUs= ++golang.org/x/image v0.0.0-20200119044424-58c23975cae1 h1:5h3ngYt7+vXCDZCup/HkCQgW5XwmSvR/nA2JmJ0RErg= ++golang.org/x/image v0.0.0-20200119044424-58c23975cae1/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0= ++golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE= ++golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc= ++golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20181114220301-adae6a3d119a/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20181220203305-927f97764cc3/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= ++golang.org/x/net v0.0.0-20190522155817-f3200d17e092/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks= ++golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U= ++golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181107165924-66b7b1311ac8/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190222072716-a9d3bda3a223/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20191026070338-33540a1f6037 h1:YyJpGZS1sBuBCzLAR1VEpK193GlqGZbnPFnPV/5Rsb4= ++golang.org/x/sys v0.0.0-20191026070338-33540a1f6037/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= ++golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= ++golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= ++google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= ++google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= ++google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c= ++google.golang.org/grpc v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= ++gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw= ++gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127 h1:qIbj1fsPNlZgppZ+VLlY7N33q108Sa+fhmuc+sWQYwY= ++gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo= ++gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74= ++gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++gopkg.in/yaml.v2 v2.2.2 h1:ZCJp+EgiOT7lHqUV2J862kp8Qj64Jo6az82+3Td9dZw= ++gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= ++ From b3eb8c624b04cb35f8d376e239e5da327416a80a Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 24 Apr 2020 10:56:55 +0200 Subject: [PATCH 181/431] added include to sanity_check_paths --- easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb | 2 +- .../easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb index 8798c2c599d..bfeb8baf6a6 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.13-foss-2018b.eb @@ -34,7 +34,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], - 'dirs': [] + 'dirs': ['include'] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb index b29291d7497..f82a40aea27 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.2.0-2.31.1.eb @@ -34,7 +34,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], - 'dirs': [] + 'dirs': ['include'] } moduleclass = 'bio' From 70747a8fb0c7e26009eb1c2dfe7e1de248b2af4b Mon Sep 17 00:00:00 2001 From: loris Date: Fri, 24 Apr 2020 11:12:33 +0200 Subject: [PATCH 182/431] Add space after intial '#' in comment --- easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb index c7a88b3cb1d..a3cbe3d6cd1 100644 --- a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb +++ b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb @@ -13,7 +13,7 @@ description = "A cross-platform software package for econometric analysis" toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'openmp': True} -#http://prdownloads.sourceforge.net/gretl/gretl-2020a.tar.xz +# http://prdownloads.sourceforge.net/gretl/gretl-2020a.tar.xz source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] sources = [SOURCELOWER_TAR_XZ] checksums = ['4c369f33c9aa825920229263bfd12560168c4e46282240bee3497436a7ae9b7b'] From dc2295443073e5a8e6ae9083828ac206aa9f7a06 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 24 Apr 2020 14:01:40 +0200 Subject: [PATCH 183/431] reworked, fixed remarks --- ...019-2020.04.13-foss-2018b-Python-3.6.6.eb} | 42 +++++++++------ .../g/goalign/goalign-0.3.2-binary.eb | 28 ---------- .../g/gotree/gotree-0.4.0-binary.eb | 28 ---------- .../i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb | 2 +- ...8b.eb => Longshot-0.4.1-GCC-7.3.0-2.30.eb} | 2 +- .../libdeflate-1.5-GCCcore-7.3.0.eb | 43 +++++++++++++++ ...b.eb => MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb} | 2 +- ...nopolish-0.13.1-foss-2018b-Python-3.6.6.eb | 53 +++++++++++++++++++ ...ampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb | 9 ++-- 9 files changed, 130 insertions(+), 79 deletions(-) rename easybuild/easyconfigs/a/artic-ncov2019/{artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb => artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb} (77%) delete mode 100644 easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb delete mode 100644 easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb rename easybuild/easyconfigs/l/Longshot/{Longshot-0.4.1-foss-2018b.eb => Longshot-0.4.1-GCC-7.3.0-2.30.eb} (96%) create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb rename easybuild/easyconfigs/m/MUSCLE/{MUSCLE-3.8.1551-foss-2018b.eb => MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb} (95%) create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb similarity index 77% rename from easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb rename to easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index ccea25cd45c..cfd5da43056 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -7,8 +7,7 @@ name = 'artic-ncov2019' # commit 4a7461c3cc9865860d69223ba8360df13a248f13 version = '2020.04.13' -local_python_versionsuffix = '-Python-%(pyver)s' -versionsuffix = local_python_versionsuffix + '-medaka' +versionsuffix = '-Python-%(pyver)s' homepage = "https://github.com/artic-network/artic-ncov2019" description = """Initial implementation of an ARTIC bioinformatics platform @@ -18,25 +17,29 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), # pandas, - ('Biopython', '1.72', local_python_versionsuffix), - ('Pysam', '0.15.1', local_python_versionsuffix), + ('Biopython', '1.72', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), ('BWA', '0.7.17'), ('Eigen', '3.3.7', '', True), ('minimap2', '2.13'), ('SAMtools', '1.9'), ('MUSCLE', '3.8.1551'), - ('ETE', '3.1.1', local_python_versionsuffix), + ('ETE', '3.1.1', versionsuffix), ('MAFFT', '7.427', '-with-extensions'), ('IQ-TREE', '1.6.12'), - ('snakemake', '5.2.4', local_python_versionsuffix), + ('snakemake', '5.2.4', versionsuffix), ('Longshot', '0.4.1'), - ('medaka', '0.11.4', local_python_versionsuffix), - ('python-parasail', '1.1.16', local_python_versionsuffix), + ('medaka', '0.11.4', versionsuffix), + ('python-parasail', '1.1.16', versionsuffix), ('PhyML', '3.3.20190321'), ('nodejs', '12.16.1'), - ('goalign', '0.3.2', '-binary', True), - ('gotree', '0.4.0', '-binary', True), - ('rampart', '1.2.0rc3', local_python_versionsuffix), + ('goalign', '0.3.2', '', True), + ('gotree', '0.4.0', '', True), + ('rampart', '1.2.0rc3', versionsuffix), + ('libdeflate', '1.5'), + ('nanopolish', '0.13.1', versionsuffix), + ('seqtk', '1.3'), + ('BCFtools', '1.9'), ] use_pip = True @@ -88,15 +91,16 @@ exts_list = [ 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], 'checksums': ['7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073'], }), + # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/Porechop/archive'], 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], }), ('binlorry', '1.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], }), ('clint', '0.5.1', { 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], @@ -108,6 +112,10 @@ exts_list = [ 'modulename': 'vcf', 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), + ('ont-fast5-api', '3.1.1', { + 'modulename': 'ont_fast5_api', + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), ] components = [ @@ -121,9 +129,11 @@ components = [ 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], }), ] - +local_artic_bins = [ + 'artic', 'artic_fasta_header', 'artic_make_depth_mask', 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' +] sanity_check_paths = { - 'files': [], + 'files': ['bin/%s' % f for f in local_artic_bins], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb deleted file mode 100644 index dacfab7ed17..00000000000 --- a/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'Binary' - -name = 'goalign' -version = '0.3.2' -versionsuffix = "-binary" - -homepage = 'https://github.com/evolbioinfo/goalign/' -description = "Goalign is a set of command line tools to manipulate multiple alignments." - -toolchain = SYSTEM - -source_urls = ['https://github.com/evolbioinfo/goalign/releases/download/v%(version)s'] -sources = ['goalign_amd64_linux'] -checksums = ['a0453c63b9c299e9d775ec9b3afe9bac33984bf14a8bcfcdbfa784e4879601d0'] - -postinstallcmds = [ - "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", -] -sanity_check_paths = { - 'files': ['%(name)s_amd64_linux'], - 'dirs': [], -} - -sanity_check_commands = [ - 'goalign --help' -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb b/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb deleted file mode 100644 index d8db557db07..00000000000 --- a/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'Binary' - -name = 'gotree' -version = '0.4.0' -versionsuffix = "-binary" - -homepage = 'https://github.com/evolbioinfo/gotree/' -description = "GoTree is a set of command line tools to manipulate phylogenetic trees." - -toolchain = SYSTEM - -source_urls = ['https://github.com/evolbioinfo/gotree/releases/download/v%(version)s'] -sources = ['gotree_amd64_linux'] -checksums = ['8527cc7082dfc46f03a1a49e02cd07da7cef94112f0b85c43de3416d53dcb188'] - -postinstallcmds = [ - "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", -] -sanity_check_paths = { - 'files': ['%(name)s_amd64_linux'], - 'dirs': [], -} - -sanity_check_commands = [ - 'gotree --help' -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb index 7a41be58181..aec8a7ac610 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'CMakeMake' name = 'IQ-TREE' version = '1.6.12' +# HTTPS is not working homepage = 'http://www.iqtree.org/' description = """Efficient phylogenomic software by maximum likelihood""" toolchain = {'name': 'foss', 'version': '2018b'} # Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary -# toolchainopts = {'usempi': True} github_account = 'Cibiv' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb similarity index 96% rename from easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb rename to easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb index f44bdff2d02..48e2eb9f6a2 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb @@ -10,7 +10,7 @@ description = """Longshot is a variant calling tool for diploid genomes using lo a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['https://github.com/pjedge/longshot/archive'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..4622b6cfa9d --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.5' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +# https://github.com/ebiggers/libdeflate +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['45b1b2332f443b705c59d06a49be009827291d2c487b076dc8ec2791eff4c711'] + +builddependencies = [ + ('binutils', '2.30'), + # ('Autotools', '20180311'), + # ('xorg-macros', '1.19.2'), +] + +skipsteps = ['configure'] +buildopts = 'PREFIX="%(installdir)s" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS"' +installopts = 'PREFIX="%(installdir)s" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS"' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb similarity index 95% rename from easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb rename to easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb index fdb6af2845b..6aff9d1e1c9 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb @@ -10,7 +10,7 @@ description = """MUSCLE is one of the best-performing multiple alignment program learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['https://www.drive5.com/muscle/'] sources = ['%(namelower)s_src_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8bfbce42b87 --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,53 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.6.5.tar.gz', 'filename': 'fast5-v0.6.5.tar.gz'}, +] +checksums = [ + '0cf0a6aea3d3b0dd81fa8877618b12bb45e2a39b2ec2fbfc6bc0df77084a7fac', # nanopolish-0.13.1.tar.gz + 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz +] + +builddependencies = [('Eigen', '3.3.7', '', True)] + +dependencies = [ + ('zlib', '1.2.11'), + ('HDF5', '1.10.2'), + ('HTSlib', '1.9'), + ('Python', '3.6.6'), + ('Biopython', '1.72', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('minimap2', '2.13'), +] + +prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb index 3f51c302b5d..112305de8b9 100644 --- a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb @@ -26,15 +26,16 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ + # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/Porechop/archive'], 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], }), ('binlorry', '1.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], }), ] @@ -58,7 +59,7 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/binlorry', 'bin/porechop'], + 'files': ['bin/binlorry', 'bin/porechop', 'bin/rampart'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ From a54bbb1e2a039c671700c38ea592f626bfd9d1be Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 24 Apr 2020 14:46:44 +0200 Subject: [PATCH 184/431] Move configs to 2019b (previous PR was a mistake) --- ...l-2019a-peigs.eb => GlobalArrays-5.7.2-intel-2019b-peigs.eb} | 2 +- ...s-5.7.2-intel-2019a.eb => GlobalArrays-5.7.2-intel-2019b.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GlobalArrays/{GlobalArrays-5.7.2-intel-2019a-peigs.eb => GlobalArrays-5.7.2-intel-2019b-peigs.eb} (96%) rename easybuild/easyconfigs/g/GlobalArrays/{GlobalArrays-5.7.2-intel-2019a.eb => GlobalArrays-5.7.2-intel-2019b.eb} (95%) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019b-peigs.eb similarity index 96% rename from easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb rename to easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019b-peigs.eb index 5a144e41ccb..772a48b7c37 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a-peigs.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019b-peigs.eb @@ -9,7 +9,7 @@ versionsuffix = '-peigs' homepage = 'https://hpc.pnl.gov/globalarrays' description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" -toolchain = {'name': 'intel', 'version': '2019a'} +toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'usempi': True} source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019b.eb similarity index 95% rename from easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb rename to easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019b.eb index a404cc5a4bc..6b85ef8f85d 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7.2-intel-2019b.eb @@ -5,7 +5,7 @@ version = '5.7.2' homepage = 'https://hpc.pnl.gov/globalarrays' description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" -toolchain = {'name': 'intel', 'version': '2019a'} +toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'usempi': True} source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] From 707a94226040e219466133bed37a1808aef2d016 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 24 Apr 2020 16:16:23 +0200 Subject: [PATCH 185/431] Create gmsh-4.5.6-foss-2019b-Python-3.7.4.eb config for gmsh 4.5.6 in foss 2019b and Python 3.7.4 --- .../gmsh-4.5.6-foss-2019b-Python-3.7.4.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..cc0d30ad086 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '4.5.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {"usempi": True} + +source_urls = ['http://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['46eaeb0cdee5822fdaa4b15f92d8d160a8cc90c4565593cfa705de90df2a463f'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('SWIG', '4.0.1'), +] + +dependencies = [ + ('Python', '3.7.4'), + ('PETSc', '3.12.4'), + ('SLEPc', '3.12.2'), +] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib64']} + +sanity_check_paths = { + 'files': ['bin/gmsh', 'lib64/gmsh.py'], + 'dirs': [], +} + +moduleclass = 'math' From 8b35e6a2c1721125cd65367ead77e3dd075695b3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 24 Apr 2020 16:16:33 +0200 Subject: [PATCH 186/431] adding easyconfigs: wxWidgets-3.1.3-GCC-8.3.0.eb --- .../GST-plugins-base-1.16.2-GCC-8.3.0.eb | 43 ++++++++++++++ .../g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb | 39 +++++++++++++ .../s/SDL2/SDL2-2.0.10-GCCcore-8.3.0.eb | 38 ++++++++++++ .../w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb | 58 +++++++++++++++++++ 4 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.10-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb new file mode 100644 index 00000000000..ca153a676c3 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.16.2' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b13e73e2fe74a4166552f9577c3dcb24bed077021b9c7fa600d910ec6987816a'] + +builddependencies = [ + ('Meson', '0.51.2', '-Python-3.7.4'), + ('Ninja', '1.9.0'), + ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), + ('gettext', '0.20.1'), + ('pkg-config', '0.29.2'), + ('Bison', '3.3.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GLib', '2.62.0'), + ('GTK+', '3.24.13'), + ('GStreamer', '1.16.2'), + ('Gdk-Pixbuf', '2.38.2'), + ('X11', '20190717'), + ('Mesa', '19.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb new file mode 100644 index 00000000000..e6c059e38f1 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.16.2' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'] + +builddependencies = [ + ('Bison', '3.3.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), + ('gettext', '0.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.62.0'), + ('zlib', '1.2.11'), + ('libunwind', '1.3.1'), +] + +configopts = '--with-dw=no ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.10-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.10-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..872b4d9b9b8 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.10-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.10' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b4656c13a1f0d0023ae2f4a9cf08ec92fffb464e0f24238337784159b8b91d57'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('X11', '20190717'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb new file mode 100644 index 00000000000..2e8fe973bf6 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.1.3' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5cb5ea326d76b5e472e9400933cef17c900d5c9b549e40eef00b64fe86d7cb0'] + +builddependencies = [ + ('gettext', '0.20.1'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.3'), + ('LibTIFF', '4.0.10'), + ('expat', '2.2.7'), + ('GTK+', '3.24.13'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('SDL2', '2.0.10'), + ('GST-plugins-base', '1.16.2'), +] + +preconfigopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-precomp-headers ' +configopts += '--disable-webkit --disable-webview --disable-webviewwebkit ' + +prebuildopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-3.1/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From d9872b3e79f6b9b8d4c2aee5a80f37167d97882e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 24 Apr 2020 16:35:31 +0200 Subject: [PATCH 187/431] Use Mesa 19.1.7 for 2019b toolchain --- .../g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb index ca153a676c3..3954ca17648 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb @@ -31,7 +31,7 @@ dependencies = [ ('GStreamer', '1.16.2'), ('Gdk-Pixbuf', '2.38.2'), ('X11', '20190717'), - ('Mesa', '19.2.1'), + ('Mesa', '19.1.7'), ] sanity_check_paths = { From c48ee705b3d43d9d296e3fe8d2c2d59e5d5887c7 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 24 Apr 2020 07:37:18 -0700 Subject: [PATCH 188/431] Update easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb --- .../r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb index d8b8292a363..bb143de556d 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['7d85fc8fc4ff96a833fa593be401aa4836b755757b518d23d4c00d7a105ce27e'] +checksums = ['f7e2bec0c2fb6837c97f5060abe0a015243d1130102a0f38807f9de0f7825de5'] use_pip = True sanity_pip_check = True From 3c1b7e3a1835420620b46e41fbf22821c65129c7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 24 Apr 2020 16:57:37 +0200 Subject: [PATCH 189/431] Fix too long line in wxWidgets-3.1.3-GCC-8.3.0.eb --- .../easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb index 2e8fe973bf6..c6de0aadaf6 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb @@ -35,7 +35,8 @@ dependencies = [ ('GST-plugins-base', '1.16.2'), ] -preconfigopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +preconfigopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0' +preconfigopts += ':$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' configopts = '--enable-intl --enable-ipv6 ' # Options required by wxPython @@ -48,7 +49,8 @@ configopts += '--enable-autoidman --with-sdl ' configopts += '--disable-precomp-headers ' configopts += '--disable-webkit --disable-webview --disable-webviewwebkit ' -prebuildopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +prebuildopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0' +prebuildopts += ':$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' sanity_check_paths = { 'files': ['bin/wx-config', 'bin/wxrc'], From df0073220597a9e13e0dc7a5143484cc20f8ccec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2020 18:17:12 +0200 Subject: [PATCH 190/431] fix Mako easyconfigs using a */2018* toolchain (cfr. #10462 --- .../Mako-1.0.7-foss-2018a-Python-2.7.14.eb | 23 ++++++++++++++----- .../Mako-1.0.7-foss-2018b-Python-2.7.15.eb | 23 ++++++++++++++----- ...Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb | 23 ++++++++++++++----- ...Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb | 23 ++++++++++++++----- .../Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb | 20 +++++++++++----- .../Mako-1.0.7-intel-2018.01-Python-2.7.14.eb | 23 ++++++++++++++----- .../Mako-1.0.7-intel-2018a-Python-2.7.14.eb | 23 ++++++++++++++----- .../Mako-1.0.7-intel-2018a-Python-3.6.4.eb | 21 +++++++++++------ .../Mako-1.0.7-intel-2018b-Python-2.7.15.eb | 23 ++++++++++++++----- .../Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb | 23 ++++++++++++++----- 10 files changed, 164 insertions(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb index 15541733fa3..87211979476 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb index 3e48251a787..56d97e4b8be 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.15')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb index 8365b65cb9d..ccdeffec3a4 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'fosscuda', 'version': '2018a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb index 0d444b57aa8..44e72fdfffc 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.15')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb index 358e9210d53..432806056ef 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,18 +9,26 @@ description = "A super-fast templating language that borrows the best ideas from toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '3.6.6')] use_pip = True -download_dep_fail = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] sanity_check_paths = { 'files': ['bin/%(namelower)s-render'], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb index 71d80846c61..546ed64cf0b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intel', 'version': '2018.01'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb index 1a9a3235d9e..ef35e7d726a 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb index 0c58ee16fbb..6f14c776574 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,19 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '3.6.4')] -download_dep_fail = True - use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb index b86532e2d46..9abe4f46098 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.15')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb index c079c1aa079..03b8a9ed736 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'iomkl', 'version': '2018a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'devel' From 79bc4ff02750806664913faa1f75030d56cc4688 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 24 Apr 2020 10:45:34 -0700 Subject: [PATCH 191/431] Update easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb Co-Authored-By: Alex Domingo --- .../root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb index 9b37593ccc4..e078d87dbe5 100644 --- a/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/root_numpy/root_numpy-4.8.0-foss-2018b-Python-3.6.6.eb @@ -18,13 +18,13 @@ checksums = [ '5842bbcde92133f60a61f56e9f0a875a0dbc2a567cc65a9ac141ecd72e416878', # root_numpy-4.8.0.tar.gz ] -use_pip = True -sanity_pip_check = True - -download_dep_fail = True dependencies = [ ('Python', '3.6.6'), ('ROOT', '6.14.06', versionsuffix), ] +use_pip = True +download_dep_fail = True +sanity_pip_check = True + moduleclass = 'math' From 514f3d78bafef32e946c78ff1b259acc0d3d114b Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 24 Apr 2020 10:46:03 -0700 Subject: [PATCH 192/431] Update easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb Co-Authored-By: Alex Domingo --- .../r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb index bb143de556d..d263ec04308 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb @@ -23,10 +23,6 @@ source_urls = ['https://github.com/rootpy/%(namelower)s/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['f7e2bec0c2fb6837c97f5060abe0a015243d1130102a0f38807f9de0f7825de5'] -use_pip = True -sanity_pip_check = True - -download_dep_fail = True dependencies = [ ('Python', '3.6.6'), ('ROOT', '6.14.06', versionsuffix), @@ -34,6 +30,10 @@ dependencies = [ ('PyTables', '3.4.4', versionsuffix), ] +use_pip = True +download_dep_fail = True +sanity_pip_check = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 74e5564a0b705f51d37e068a94ef3466c2c6dc12 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 24 Apr 2020 10:46:18 -0700 Subject: [PATCH 193/431] Update easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb Co-Authored-By: Alex Domingo --- .../r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb index d263ec04308..bb78f51a399 100644 --- a/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rootpy/rootpy-1.0.1-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ download_dep_fail = True sanity_pip_check = True sanity_check_paths = { - 'files': [], + 'files': ['bin/roosh', 'bin/root2hdf5', 'bin/rootpy'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From daf177b7bbdf008ee39a1419f14a09b10f27583a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2020 20:03:50 +0200 Subject: [PATCH 194/431] adding easyconfigs: BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb, spaln-2.4.03-iccifort-2019.5.281.eb, Exonerate-2.4.0-iccifort-2019.5.281.eb, GeneMark-ET-4.57-GCCcore-8.3.0.eb, GenomeThreader-1.7.3-Linux_x86_64-64bit.eb --- .../BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb | 41 +++++++++++++++++++ .../Exonerate-2.4.0-iccifort-2019.5.281.eb | 37 +++++++++++++++++ .../GeneMark-ET-4.57-GCCcore-8.3.0.eb | 27 ++++++++++++ ...GenomeThreader-1.7.3-Linux_x86_64-64bit.eb | 21 ++++++++++ .../spaln/spaln-2.4.03-iccifort-2019.5.281.eb | 31 ++++++++++++++ 5 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2019.5.281.eb create mode 100644 easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.57-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.03-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..e356a0da97b --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'BRAKER' +version = '2.1.5' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://github.com/Gaius-Augustus/BRAKER' +description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET + and AUGUSTUS in novel eukaryotic genomes.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['528507c4fe3335865ead5421341f6e77959d2d327183b6c59d0858e6869d7ace'] + +dependencies = [ + ('Perl', '5.30.0'), + ('AUGUSTUS', '3.3.3'), + ('GeneMark-ET', '4.57'), + ('BamTools', '2.5.1'), + ('SAMtools', '1.10'), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', True), + ('spaln', '2.4.03'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.9.0'), + ('Biopython', '1.75', versionsuffix), +] + +fix_perl_shebang_for = ['scripts/*.pl'] + +sanity_check_paths = { + 'files': ['scripts/align2hints.pl', 'scripts/braker.pl', 'scripts/findGenesInIntrons.pl', 'scripts/startAlign.pl'], + 'dirs': ['docs', 'example'], +} + +sanity_check_commands = ["braker.pl --help"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2019.5.281.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..41b2442ffdc --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2019.5.281.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GLib', '2.62.0')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.57-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.57-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7881a51a617 --- /dev/null +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.57-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'GeneMark-ET' +version = '4.57' + +homepage = 'http://exon.gatech.edu/GeneMark' +description = "Eukaryotic gene prediction suite with automatic training" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +# download via http://exon.gatech.edu/GeneMark/license_download.cgi +# rename gmes_linux_64.tar.gz to gmes_linux_64-4.57.tar.gz +sources = ['gmes_linux_64-4.57.tar.gz'] +checksums = ['29d142d98a60774411c191e26a042173679dccbc1c830b3e34156078e4040d9c'] + +dependencies = [('Perl', '5.30.0')] + +fix_perl_shebang_for = ['*.pl'] + +sanity_check_paths = { + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb b/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb new file mode 100644 index 00000000000..dd9fd8fbd67 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'GenomeThreader' +version = '1.7.3' +versionsuffix = '-Linux_x86_64-64bit' + +homepage = 'http://genomethreader.org' +description = "GenomeThreader is a software tool to compute gene structure predictions." + +toolchain = SYSTEM + +source_urls = ['http://genomethreader.org/distributions/'] +sources = ['gth-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['cdcf7f0c642c14c9dc6b9270e3172de96696f42c25185beabc9a1f68c9c41a57'] + +sanity_check_paths = { + 'files': ['bin/gth', 'bin/gthbssmbuild', 'bin/gthsplit'], + 'dirs': ['bin/bssm', 'bin/gthdata'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.03-iccifort-2019.5.281.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.03-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..d60b76970b7 --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.03-iccifort-2019.5.281.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.03' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['Ver.%(version)s.tar.gz'] +checksums = ['6b7d19392485827b1711bbafdd9305d6ed33f92b4e4ba8ec0cfad4dc20364b23'] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +moduleclass = 'bio' From abf9663357a56a23ddcad3505c291e1b9eac8d94 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 24 Apr 2020 20:24:16 +0200 Subject: [PATCH 195/431] adding easyconfigs: NWChem-7.0.0-intel-2019b-Python-3.7.4.eb and patches: NWChem-7.0.0_external-ga-peigs-flag.patch --- .../NWChem-7.0.0-intel-2019b-Python-3.7.4.eb | 49 +++++++++++++++++++ .../NWChem-7.0.0_external-ga-peigs-flag.patch | 13 +++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.0_external-ga-peigs-flag.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..92adaf8b52e --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,49 @@ +name = 'NWChem' +version = '7.0.0' +versionsuffix = '-Python-%(pyver)s' +local_verdate = '2020-02-26' +local_revision = '2c9a1c7c' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'i8': True} + +source_urls = ['https://github.com/nwchemgit/nwchem/releases/download/v%(version)s-release/'] +sources = ['nwchem-%%(version)s-release.revision-%s-src.%s.tar.bz2' % (local_revision, local_verdate)] +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-7.0.0_external-ga-peigs-flag.patch', +] +checksums = [ + # nwchem-7.0.0-release.revision-2c9a1c7c-src.2020-02-26.tar.bz2 + '1046e13a4c7f95860c8e8fac2b4d80657900ecd07a8242943d564048ce303514', + '215ec54f6132f2c9306bd636456722a36f0f1d98a67a0c8cbd10c5d1eed68feb', # NWChem_fix-date.patch + '68d6e3f8d71635a9a4fb2ec07cdcf18683598358ccc4c3a01c2da8e36ebc8c0a', # NWChem-7.0.0_external-ga-peigs-flag.patch +] + +dependencies = [ + ('GlobalArrays', '5.7.2', '-peigs'), + ('Python', '3.7.4'), +] + +# This easyconfig is using the default for armci_network (OPENIB) and +# thus needs infiniband libraries. +#osdependencies = [ +# ('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'), +# ('libibumad-dev', 'libibumad-devel', 'rdma-core-devel'), +#] + +preconfigopts = 'export EXTRA_LIBS=-lutil && ' +#buildopts = 'LDFLAGS="$LDFLAGS -lutil"' + +modules = 'all python' + +moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0_external-ga-peigs-flag.patch b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0_external-ga-peigs-flag.patch new file mode 100644 index 00000000000..3e58b0ff409 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0_external-ga-peigs-flag.patch @@ -0,0 +1,13 @@ +# Fixes incorrect peigs checking flag for ga-config +# Author: Mikael Öhman +--- src/config/makefile.h.orig 2020-04-24 19:42:34.310637564 +0200 ++++ src/config/makefile.h 2020-04-24 19:44:09.418426211 +0200 +@@ -110,7 +110,7 @@ + $(error ) + endif + #check peigs interface +- GA_HAS_PEIGS = $(shell ${EXTERNAL_GA_PATH}/bin/ga-config --enable-peigs | awk '/yes/ {print "Y"}') ++ GA_HAS_PEIGS = $(shell ${EXTERNAL_GA_PATH}/bin/ga-config --use_peigs | awk '/1/ {print "Y"}') + GA_HAS_SCALAPACK = $(shell ${EXTERNAL_GA_PATH}/bin/ga-config --use_scalapack | awk '/1/ {print "Y"}') + ifneq ($(GA_HAS_PEIGS),Y) + ifneq ($(GA_HAS_SCALAPACK),Y) From 578a6caa8b5147fd4c31bbd699c981a9cd07dc7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Apr 2020 21:08:17 +0200 Subject: [PATCH 196/431] use https:// in homepage in Mako easyconfigs --- .../easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb | 2 +- .../m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb | 2 +- .../m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb | 2 +- .../m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb | 2 +- .../m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb index 87211979476..c705394e03b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'foss', 'version': '2018a'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb index 56d97e4b8be..ff45921f9e8 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb index ccdeffec3a4..fc3215a0712 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'fosscuda', 'version': '2018a'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb index 44e72fdfffc..4366ca55fea 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'fosscuda', 'version': '2018b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb index 432806056ef..eb6febf4b63 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.%(namelower)stemplates.org' +homepage = 'https://www.makotemplates.org' description = "A super-fast templating language that borrows the best ideas from the existing templating languages" toolchain = {'name': 'fosscuda', 'version': '2018b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb index 546ed64cf0b..e95ac36a974 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018.01-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2018.01'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb index ef35e7d726a..426de8784bc 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2018a'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb index 6f14c776574..f1310f736ff 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2018a'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb index 9abe4f46098..031d3d2df99 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2018b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb index 03b8a9ed736..5a0ec8a6856 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-iomkl-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'iomkl', 'version': '2018a'} From 430fa75a3c4b6d40c9ff04bd88b30380771bba24 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Sat, 25 Apr 2020 09:19:22 +0200 Subject: [PATCH 197/431] protobuf-python installation fails with pip --- .../protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb index 62fc89ee0b2..4f45605d83d 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2019b-Python-3.7.4.eb @@ -20,6 +20,10 @@ dependencies = [ start_dir = 'python' +download_dep_fail = True +use_pip = False # installation fails with pip +sanity_pip_check = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From fa116c036f6c8bd6e93781581417d77ee4eac166 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 25 Apr 2020 12:02:43 +0200 Subject: [PATCH 198/431] Add some missing dependencies for wxWidgets-3.1.3 --- .../w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb index c6de0aadaf6..6fd042def34 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb @@ -20,23 +20,31 @@ checksums = ['a5cb5ea326d76b5e472e9400933cef17c900d5c9b549e40eef00b64fe86d7cb0'] builddependencies = [ ('gettext', '0.20.1'), + ('pkg-config', '0.29.2'), ] dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.3'), + ('XZ', '5.2.4'), + ('jbigkit', '2.1'), ('LibTIFF', '4.0.10'), ('expat', '2.2.7'), ('GTK+', '3.24.13'), + ('X11', '20190717'), ('Mesa', '19.1.7'), ('libGLU', '9.0.1'), ('SDL2', '2.0.10'), + ('cairo', '1.16.0'), + ('GStreamer', '1.16.2'), ('GST-plugins-base', '1.16.2'), + ('GLib', '2.62.0'), ] -preconfigopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0' -preconfigopts += ':$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext configopts = '--enable-intl --enable-ipv6 ' # Options required by wxPython @@ -46,15 +54,14 @@ configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' configopts += '--enable-mediactrl --enable-display --enable-geometry ' configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' configopts += '--enable-autoidman --with-sdl ' -configopts += '--disable-precomp-headers ' configopts += '--disable-webkit --disable-webview --disable-webviewwebkit ' -prebuildopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0' -prebuildopts += ':$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext sanity_check_paths = { 'files': ['bin/wx-config', 'bin/wxrc'], - 'dirs': ['include/wx-3.1/wx', 'lib', 'share'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], } moduleclass = 'vis' From 6bc2360d755da6ddd219c1147400c92755afe48e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 25 Apr 2020 13:11:27 +0200 Subject: [PATCH 199/431] Add some missing dependencies for GStreamer-1.16.2 --- .../easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb index e6c059e38f1..92e0c55eca2 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb @@ -24,8 +24,11 @@ builddependencies = [ ] dependencies = [ - ('GLib', '2.62.0'), ('zlib', '1.2.11'), + ('GMP', '6.1.2'), + ('GSL', '2.6'), + ('GLib', '2.62.0'), + ('GTK+', '3.24.13'), ('libunwind', '1.3.1'), ] From 805c11654dc5c34227786b692622ded2af4c7869 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 25 Apr 2020 13:16:28 +0200 Subject: [PATCH 200/431] Add some more missing dependencies for wxWidgets-3.1.3 --- .../easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb index 6fd042def34..8c56bfcbff0 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.3-GCC-8.3.0.eb @@ -21,6 +21,7 @@ checksums = ['a5cb5ea326d76b5e472e9400933cef17c900d5c9b549e40eef00b64fe86d7cb0'] builddependencies = [ ('gettext', '0.20.1'), ('pkg-config', '0.29.2'), + ('Python', '3.7.4'), ] dependencies = [ @@ -37,7 +38,6 @@ dependencies = [ ('libGLU', '9.0.1'), ('SDL2', '2.0.10'), ('cairo', '1.16.0'), - ('GStreamer', '1.16.2'), ('GST-plugins-base', '1.16.2'), ('GLib', '2.62.0'), ] @@ -49,6 +49,8 @@ preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext configopts = '--enable-intl --enable-ipv6 ' # Options required by wxPython configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above configopts += '--with-opengl ' configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' configopts += '--enable-mediactrl --enable-display --enable-geometry ' From 371be51927fc90e03a3481247c92a92a370f1049 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 25 Apr 2020 13:17:31 +0200 Subject: [PATCH 201/431] Add some more missing dependencies for wxWidgets-3.1.3 --- .../j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..56ad0a98b56 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb @@ -0,0 +1,46 @@ +# EasyBuild easyconfig +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = '' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' From 336ac423813105bcb42b4672c73c3ef0b7f266a3 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 25 Apr 2020 20:59:19 +0200 Subject: [PATCH 202/431] Cleanup --- .../n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb index 92adaf8b52e..7c7df2bd485 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb @@ -33,15 +33,7 @@ dependencies = [ ('Python', '3.7.4'), ] -# This easyconfig is using the default for armci_network (OPENIB) and -# thus needs infiniband libraries. -#osdependencies = [ -# ('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel'), -# ('libibumad-dev', 'libibumad-devel', 'rdma-core-devel'), -#] - preconfigopts = 'export EXTRA_LIBS=-lutil && ' -#buildopts = 'LDFLAGS="$LDFLAGS -lutil"' modules = 'all python' From a2e8c81da87b6f78e8acba450e71551221d1494b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 25 Apr 2020 21:22:01 +0200 Subject: [PATCH 203/431] W391 fix --- .../n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb index 7c7df2bd485..791e0dc8351 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb @@ -38,4 +38,3 @@ preconfigopts = 'export EXTRA_LIBS=-lutil && ' modules = 'all python' moduleclass = 'chem' - From 4c066e21516c2b4437c82a1020f0136b1d1b59ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2020 08:33:35 +0200 Subject: [PATCH 204/431] {toolchain} foss/2020a --- .../f/FFTW/FFTW-3.3.8-gompi-2020a.eb | 17 +++++++ easybuild/easyconfigs/f/foss/foss-2020a.eb | 27 +++++++++++ easybuild/easyconfigs/g/GCC/GCC-9.3.0.eb | 22 +++++++++ easybuild/easyconfigs/g/gompi/gompi-2020a.eb | 20 ++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2020a.eb | 21 ++++++++ .../h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb | 48 +++++++++++++++++++ .../libpciaccess-0.16-GCCcore-9.3.0.eb | 26 ++++++++++ .../l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb | 28 +++++++++++ .../n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb | 34 +++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb | 28 +++++++++++ .../o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb | 24 ++++++++++ .../ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb | 17 +++++++ .../xorg-macros-1.19.2-GCCcore-9.3.0.eb | 37 ++++++++++++++ 13 files changed, 349 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2020a.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2020a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020a.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020a.eb new file mode 100644 index 00000000000..1e3dfaa89ad --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompi-2020a.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2020a.eb b/easybuild/easyconfigs/f/foss/foss-2020a.eb new file mode 100644 index 00000000000..2b0739b47c8 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2020a.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2020a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '9.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.0.3', '', ('GCC', local_gccver)), + ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GCC/GCC-9.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-9.3.0.eb new file mode 100644 index 00000000000..0489a3aa7a0 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-9.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '9.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.34', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2020a.eb b/easybuild/easyconfigs/g/gompi/gompi-2020a.eb new file mode 100644 index 00000000000..15ee0f5a7cc --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2020a.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2020a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '9.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.0.3', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020a.eb new file mode 100644 index 00000000000..975ddeef5a8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2020a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a109e5d7a9b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.2.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2defba03ddd91761b858cbbdc2e3a6e27b44e94696dbfa21380191328485a433'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('numactl', '2.0.13'), + ('libxml2', '2.9.10'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a5f69896b65 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-9.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.16' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..53b484f969b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.10' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8bbab9492c6 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.13' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97ee012b2f294903530424b4ff7f28bcaad6a356897ce8777383f87e5c2e325d'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb new file mode 100644 index 00000000000..911b346109c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.9' + +homepage = 'https://xianyi.github.com/OpenBLAS/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + '17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380', # v0.3.9.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb new file mode 100644 index 00000000000..6426e2d34ca --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb @@ -0,0 +1,24 @@ +name = 'OpenMPI' +version = '4.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0') +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb new file mode 100644 index 00000000000..5ed0ad1f454 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a.eb @@ -0,0 +1,17 @@ +name = 'ScaLAPACK' +version = '2.1.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] + +dependencies = [('OpenBLAS', '0.3.9')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..35d18f46f79 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.2' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From ad7786acc3350ee876a13fd236ab5a02287f3633 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2020 11:39:17 +0200 Subject: [PATCH 205/431] adding easyconfigs: Python-2.7.18-GCCcore-9.3.0.eb --- .../p/Python/Python-2.7.18-GCCcore-9.3.0.eb | 296 ++++++++++++++++++ 1 file changed, 296 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f3bd9362a8b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0.eb @@ -0,0 +1,296 @@ +name = 'Python' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +dependencies = [ + ('binutils', '2.34'), # required for pip install that involves compilation + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.31.1'), + ('GMP', '6.2.0'), # required for pycrypto + ('libffi', '3.3'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1e'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 23 April 2020 +exts_list = [ + # setuptools 44.0.0 is the most recent version still supporting Python 2.x + ('setuptools', '44.0.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'use_pip': False, + 'checksums': ['e5baf7723e5bb8382fc146e33032b241efc63314211a3a120aaa55d62d2bb008'], + }), + ('pip', '20.0.2', { + 'use_pip': False, + 'checksums': ['7db0c8ea4c7ea51c8049640e8e6e7fde949de672bfa4949920675563a5a6967f'], + }), + ('wheel', '0.34.2', { + 'checksums': ['8788e9155fe14f54164c1b9eb0a319d98ef02c160725587ad60f14ddc57b6f96'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.4.5', { + 'checksums': ['07f558fece33b05caf857474a366dfcc00562bca13dd8b47b2b3e22d9f9bf55c'], + }), + ('Cython', '0.29.16', { + 'checksums': ['232755284f942cbb3b43a06cd85974ef3c970a021aef19b5243c03ee2b08fa05'], + }), + ('six', '1.14.0', { + 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], + }), + ('toml', '0.10.0', { + 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], + }), + ('setuptools_scm', '3.5.0', { + 'checksums': ['5bdf21a05792903cafe7ae0c9501182ab52497614fa6b1750d9dbae7b60c1a87'], + }), + ('python-dateutil', '2.8.1', { + 'modulename': 'dateutil', + 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.4.0', { + 'modulename': 'arff', + 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.15', { + 'checksums': ['8f12ac317f8a1318efa75757ef0a651abe12e51fc1af8838fb91079445227277'], + }), + ('enum34', '1.1.10', { + 'modulename': 'enum', + 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.3.0', { + 'checksums': ['5a215cb8dc12f892244e3a113fe05397ee23c5c4ca7a69cd6e69811755efc42d'], + }), + ('idna', '2.9', { + 'checksums': ['7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb'], + }), + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + ('cffi', '1.14.0', { + 'checksums': ['2d384f4a127a15ba701207f7639d94106693b6cd64173d6c8988e2c25f3ac2b6'], + }), + ('cryptography', '2.9.2', { + 'checksums': ['a0c30272fb4ddda5f5ffc1089d7405b7a71b0b0f51993cb4e5dbb4590b2fc229'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.3.0', { + 'modulename': 'nacl', + 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + }), + ('bcrypt', '3.1.7', { + 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], + }), + ('paramiko', '2.7.1', { + 'checksums': ['920492895db8013f6cc0179293147f830b8c7b21fdfc839b6bad760c27459d9f'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.10.9', { + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.7.19', { + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + # mock 3.0.5 is the most recent version still supporting Python 2.x + ('mock', '3.0.5', { + 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], + }), + ('pytz', '2019.3', { + 'checksums': ['b02c06db6cf09c12dd25137e563b31700d3b80fcc4ad23abb7a315f2789819be'], + }), + ('bitstring', '3.1.6', { + 'checksums': ['c97a8e2a136e99b523b27da420736ae5cb68f83519d633794a6a11192f69f8bf'], + }), + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('distlib', '0.3.0', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['2e166e231a26b36d6dfe35a48c4464346620f8645ed0ace01ee31822b288de21'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('importlib_resources', '1.4.0', { + 'checksums': ['4019b6a9082d8ada9def02bece4a76b131518866790d58fdda0b5f8c603b36c2'], + }), + ('virtualenv', '20.0.18', { + 'checksums': ['ac53ade75ca189bc97b6c1d9ec0f1a50efe33cbf178ae09452dcd9fd309013c1'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.14.1', { + 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], + }), + ('chardet', '3.0.4', { + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2020.4.5.1', { + 'checksums': ['51fcb31174be6e6664c5f69e3e1691a2d72a1a12e90f872cbdb1567eb47b6519'], + }), + ('urllib3', '1.25.9', { + 'checksums': ['3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527'], + }), + ('requests', '2.23.0', { + 'checksums': ['b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.9', { + 'checksums': ['d80a948f91f78d08f789b0a7c3fb2bd9a34ad625f5ce88c262a6c91189a4abb9'], + }), + ('tabulate', '0.8.7', { + 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], + }), + ('ujson', '2.0.3', { + 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], + }), + ('atomicwrites', '1.3.0', { + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('py', '1.8.1', { + 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + # zipp 1.2.0 is the most recent version still supporting Python 2.x + ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], + }), + # configparser 4.0.2 is the most recent version still supporting Python 2.x + ('configparser', '4.0.2', { + 'checksums': ['c7d282687a5308319bf3d2e7706e575c635b0a470342641c93bea0ea3b5331df'], + }), + ('contextlib2', '0.6.0.post1', { + 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], + }), + ('importlib_metadata', '1.6.0', { + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + # more-itertools 5.0.0 is the most recent version still supporting Python 2.x + ('more-itertools', '5.0.0', { + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('wcwidth', '0.1.9', { + 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], + }), + # pytest 4.6.9 is the most recent version still supporting Python 2.x + ('pytest', '4.6.9', { + 'checksums': ['19e8f75eac01dd3f211edd465b39efbcbdc8fc5f7866d7dd49fedb30d8adf339'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('packaging', '20.3', { + 'checksums': ['3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3'], + }), + # sphinxcontrib-websupport 1.1.2 is the most recent version still supporting Python 2.x + ('sphinxcontrib-websupport', '1.1.2', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc'], + }), + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], + }), + ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.7.4.1', { + 'checksums': ['91dfe6f3f706ee8cc32d38edbbf304e9b7583fb37108fef38229617f8b3eba23'], + }), + # Sphinx 1.8.5 is the most recent version still supporting Python 2.x + ('Sphinx', '1.8.5', { + 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], + }), + ('click', '7.1.1', { + 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], + }), + ('psutil', '5.7.0', { + 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('singledispatch', '3.4.0.3', { + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), +] + +moduleclass = 'lang' From 8bba295ec11182dd34f94ec0bc90b0245ef2436e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2020 15:32:36 +0200 Subject: [PATCH 206/431] {vis}[GCCcore/9.3.0] X11 v20200222 --- .../fontconfig-2.13.92-GCCcore-9.3.0.eb | 39 ++++ .../freetype/freetype-2.10.1-GCCcore-9.3.0.eb | 37 ++++ .../g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb | 32 +++ .../intltool/intltool-0.51.0-GCCcore-9.3.0.eb | 33 +++ ...Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb | 36 +++ .../n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb | 29 +++ .../pkg-config-0.29.2-GCCcore-9.3.0.eb | 34 +++ .../x/X11/X11-20200222-GCCcore-9.3.0.eb | 208 ++++++++++++++++++ 8 files changed, 448 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e98c515a9ac --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.13.92' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3406a05b83a42231e3df68d02bc0a0cf47b3f2e8f11c8ede62267daf5f130016'] + +builddependencies = [ + ('binutils', '2.34'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('freetype', '2.10.1'), + ('util-linux', '2.35'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..ac1804734f4 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.1-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +name = 'freetype' +version = '2.10.1' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3a60d391fd579440561bf0e7f31af2222bc610ad6ce4d9d7bd2165bca8669110'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..27b89d2bef1 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.20.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..284ffe7421e --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('Perl', '5.30.2'), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..17a996d83b5 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.53.2-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.53.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3e8f830f33184397c2eb0b651ec502adb63decb28978bdc84b3558d71284c21f'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('Ninja', '1.10.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cfd71248ed2 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.0-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.10.0' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3810318b08489435f8efc19c05525e80a993af5a55baa0dfeae0465a9d45f99f'] + +builddependencies = [ + ('binutils', '2.34'), + ('Python', '3.8.2'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..9aca10ce415 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.34')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c0134438868 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb @@ -0,0 +1,208 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20200222' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('Bison', '3.5.3'), + ('gettext', '0.20.1'), + ('pkg-config', '0.29.2'), + ('intltool', '0.51.0'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.13.92'), + ('freetype', '2.10.1'), + ('zlib', '1.2.11'), + ('xorg-macros', '1.19.2'), + ('libpciaccess', '0.16'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2019.2', { # 2019-10-17 + 'checksums': ['ebfcfce48b66bec25d5dff0e9510e04053ef78e51a8eabeeee4c00e399226d61'], + }), + ('libXau', '1.0.9', { # 2019-02-10 + 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.14', { # 2020-02-22 + 'checksums': ['1c3fa23d091fb5e4f1e9bf145a902161cec00d260fabf880a7a248b02ab27031'], + }), + ('libxcb', '1.14', { # 2020-02-22 + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2c7fcddd1da34d9b238c9caeda20d3bd7486456fc50b3cc6567185dbd5b0ad02'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '0.10.0', { # 2020-01-18 + 'easyblock': 'MesonNinja', + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'checksums': ['57c3630cdc38fb4734cd57fa349e92244f5ae3862813e533cedbd86721a0b6f2'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.6.9', { # 2019-10-09 + 'checksums': ['b8c0930a9b25de15f3d773288cacd5e2f0a4158e194935615c52aeceafd1107b'], + }), + ('libXext', '1.3.4', { # 2019-03-16 + 'checksums': ['8ef0789f282826661ff40a8eef22430378516ac580167da35cc948be9041aac1'], + }), + ('libFS', '1.0.8', { # 2019-03-10 + 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.0', { # 2019-06-21 + 'checksums': ['d4bee88898fc5e1dc470e361430c72fbc529b9cdbbb6c0ed3affea3a39f97d8d'], + }), + ('libXmu', '1.1.3', { # 2019-03-16 + 'checksums': ['5bd9d4ed1ceaac9ea023d86bf1c1632cd3b172dce4a193a72a94e1d9df87a62e'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.13', { # 2015-05-01 + 'checksums': ['7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694'], + }), + ('libXfixes', '5.0.3', { # 2016-10-04 + 'checksums': ['9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.10', { # 2016-10-04 + 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], + }), + ('libXcursor', '1.2.0', { # 2019-03-11 + 'checksums': ['ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.4', { # 2019-02-20 + 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.3', { # 2019-09-14 + 'checksums': ['a4b761a37528353a2b83dba364d7c1fd6aef2d554a1a019815f24f7f8866890e'], + }), + ('libXft', '2.3.3', { # 2019-03-16 + 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], + }), + ('libXi', '1.7.10', { # 2019-06-19 + 'checksums': ['b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3'], + }), + ('libXinerama', '1.1.4', { # 2018-07-05 + 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.0', { # 2017-10-11 + 'checksums': ['5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a'], + }), + ('libXtst', '1.2.3', { # 2016-10-04 + 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.12', { # 2019-09-24 + 'checksums': ['024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.4', { # 2015-02-24 + 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.0', { # 2019-03-16 + 'checksums': ['2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.0', { # 2014-10-15 + 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], + }), + ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 + 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], + }), + ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 + 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], + }), + ('xcb-util-wm', '0.4.1', { # 2014-02-19 + 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], + }), + ('xcb-util-cursor', '0.1.3', { # 2016-05-12 + 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], + }), + ('xkeyboard-config', '2.28', { # 2019-10-19 + 'checksums': ['4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff'], + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.3', { # 2015-02-21 + 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 5a1df9df5d2970c95ba739db4fa773e9847ba448 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2020 15:56:19 +0200 Subject: [PATCH 207/431] add missing easyconfigs for gperf, libpng and util-linux --- .../g/gperf/gperf-3.1-GCCcore-9.3.0.eb | 29 +++++++++++++ .../l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb | 31 ++++++++++++++ .../util-linux-2.35-GCCcore-9.3.0.eb | 41 +++++++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8f058bba931 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' + +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c0e8bbb3edd --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-9.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('zlib', '1.2.11')] + +local_majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f124a23240f --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.35-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.35' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98acab129a8490265052e6c1e033ca96d68758a13bb7fcd232c06bf16cc96238'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 85e74a6791cca7a030a34485022bf0028b6c6b49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2020 16:10:26 +0200 Subject: [PATCH 208/431] {data}[gompi/2020a] HDF5 v1.10.6 --- .../h/HDF5/HDF5-1.10.6-gompi-2020a.eb | 21 ++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb | 29 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-gompi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-gompi-2020a.eb new file mode 100644 index 00000000000..270b74dd8d1 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-gompi-2020a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.6' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..242c281b919 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' From 6e9f8bc538f01f4b7d647d0e501aa71059ceb452 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Apr 2020 16:17:22 +0200 Subject: [PATCH 209/431] {devel}[GCCcore/9.3.0] CMake v3.16.4 --- .../c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb | 35 +++++++++++++ .../c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb | 49 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e36b56522ed --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.16.4-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +name = 'CMake' +version = '3.16.4' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9bcc8c114d9da603af9512083ed7d4a39911d16105466beba165ba8fe939ac2c'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.69.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..71ff6909f25 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.69.1-GCCcore-9.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.69.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['01ae0c123dee45b01bbaef94c0bc00ed2aec89cb2ee0fd598e0d302a6b5e0a98'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d') +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +configopts = '--with-zlib' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From b6a4180f3efa2c9f4c5804ac024a66857eb7bdbb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 26 Apr 2020 17:07:28 +0200 Subject: [PATCH 210/431] make suggested changes --- ...019b-Python-3.7.4.eb => gmpy2-2.1.0b4-GCC-8.3.0.eb} | 10 +++++----- ...{MPC-1.1.0-foss-2019b.eb => MPC-1.1.0-GCC-8.3.0.eb} | 2 +- .../s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/g/gmpy2/{gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb => gmpy2-2.1.0b4-GCC-8.3.0.eb} (65%) rename easybuild/easyconfigs/m/MPC/{MPC-1.1.0-foss-2019b.eb => MPC-1.1.0-GCC-8.3.0.eb} (94%) diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb similarity index 65% rename from easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb index bb990a023c7..de42ebc2374 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b4-GCC-8.3.0.eb @@ -1,20 +1,20 @@ easyblock = 'PythonPackage' name = 'gmpy2' -version = '2.1.0b1' -versionsuffix = '-Python-%(pyver)s' +version = '2.1.0b4' homepage = 'https://github.com/aleaxit/gmpy' description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" -toolchain = {'name': 'foss', 'version': '2019b'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['30b30707c782e4e355c920d1d998751ffc1b2189070a88a482f08c6e35511939'] +checksums = ['9564deb6dcc7045749c0c5d73b23855ef6220c60b4cc6ffa4b1e0b1b1ee95eaf'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Python', '3.7.4'), ('GMP', '6.1.2'), ('MPFR', '4.0.2'), ('MPC', '1.1.0'), diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb b/easybuild/easyconfigs/m/MPC/MPC-1.1.0-GCC-8.3.0.eb similarity index 94% rename from easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb rename to easybuild/easyconfigs/m/MPC/MPC-1.1.0-GCC-8.3.0.eb index 3db55bfdb58..9582cd0df2b 100644 --- a/easybuild/easyconfigs/m/MPC/MPC-1.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/m/MPC/MPC-1.1.0-GCC-8.3.0.eb @@ -12,7 +12,7 @@ description = """Gnu Mpc is a C library for the arithmetic of operation. At the same time, speed of operation at high precision is a major design goal.""" -toolchain = {'name': 'foss', 'version': '2019b'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb index 3de30912703..9b1e7b6a9d1 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.5.1-foss-2019b-Python-3.7.4.eb @@ -23,7 +23,7 @@ checksums = [ dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), - ('gmpy2', '2.1.0b1', versionsuffix), + ('gmpy2', '2.1.0b4'), ] download_dep_fail = True From 9daefe34863f670ae4d8734a8d0407454328640b Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 26 Apr 2020 15:54:13 +0000 Subject: [PATCH 211/431] Add -PyTorch-1.4.0 versionsuffix --- ...sion-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/torchvision/{torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb => torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb} (80%) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb similarity index 80% rename from easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb index c7150d6d3ab..5bf774e6e86 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -2,7 +2,8 @@ easyblock = 'PythonPackage' name = 'torchvision' version = '0.5.0' -versionsuffix = '-Python-%(pyver)s' +local_pytorch_ver = '1.4.0' +versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_ver homepage = 'https://github.com/pytorch/vision' description = " Datasets, Transforms and Models specific to Computer Vision" @@ -15,10 +16,11 @@ checksums = ['eb9afc93df3d174d975ee0914057a9522f5272310b4d56c150b955c287a4d74d'] builddependencies = [('CMake', '3.15.3')] +local_pysuff = '-Python-%(pyver)s' dependencies = [ ('Python', '3.7.4'), ('Pillow-SIMD', '6.0.x.post0'), - ('PyTorch', '1.4.0', versionsuffix), + ('PyTorch', '1.4.0', local_pysuff), ] use_pip = True From 4ef4a584521e8c8ff2ecfa4eedfc2255c877615d Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 26 Apr 2020 16:33:40 +0000 Subject: [PATCH 212/431] Add sanity_pip_check --- ...orchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb index 5bf774e6e86..42be229cf23 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -25,6 +25,7 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True sanity_check_paths = { 'files': [], From 855ed9054b30c8c7afacf2d538ed5a5789ab0270 Mon Sep 17 00:00:00 2001 From: crubb Date: Sun, 26 Apr 2020 19:38:04 +0200 Subject: [PATCH 213/431] Apply suggestions from code review Co-Authored-By: Alex Domingo --- ...0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb index 42be229cf23..d87d227ec79 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -2,8 +2,7 @@ easyblock = 'PythonPackage' name = 'torchvision' version = '0.5.0' -local_pytorch_ver = '1.4.0' -versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_ver +versionsuffix = '-Python-%(pyver)s-PyTorch-1.4.0' homepage = 'https://github.com/pytorch/vision' description = " Datasets, Transforms and Models specific to Computer Vision" @@ -16,20 +15,14 @@ checksums = ['eb9afc93df3d174d975ee0914057a9522f5272310b4d56c150b955c287a4d74d'] builddependencies = [('CMake', '3.15.3')] -local_pysuff = '-Python-%(pyver)s' dependencies = [ ('Python', '3.7.4'), ('Pillow-SIMD', '6.0.x.post0'), - ('PyTorch', '1.4.0', local_pysuff), + ('PyTorch', '1.4.0', '-Python-%(pyver)s'), ] use_pip = True download_dep_fail = True sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/torchvision'], -} - moduleclass = 'vis' From 1178116e129be2570596d01b09b29110bfb09dc9 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Sun, 26 Apr 2020 21:25:42 +0200 Subject: [PATCH 214/431] Update gmsh-4.5.6-foss-2019b-Python-3.7.4.eb Update of homepage and download page to https --- .../easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb index cc0d30ad086..084572f20f1 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.5.6-foss-2019b-Python-3.7.4.eb @@ -4,13 +4,13 @@ name = 'gmsh' version = '4.5.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://geuz.org/gmsh' +homepage = 'https://gmsh.info/' description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {"usempi": True} -source_urls = ['http://gmsh.info/src/'] +source_urls = ['https://gmsh.info/src/'] sources = ['%(name)s-%(version)s-source.tgz'] checksums = ['46eaeb0cdee5822fdaa4b15f92d8d160a8cc90c4565593cfa705de90df2a463f'] From bdce278af75f8cbfe8aa54ec8c02d54cc96edd6e Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Sun, 26 Apr 2020 21:33:00 +0200 Subject: [PATCH 215/431] Included update of older confige to https pages --- .../easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb | 4 ++-- .../easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb | 4 ++-- .../easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb index 78928684692..c3bfdf84a6a 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb @@ -4,13 +4,13 @@ name = 'gmsh' version = '3.0.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://geuz.org/gmsh' +homepage = 'https://gmsh.info/' description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {"usempi": True} -source_urls = ['http://gmsh.info/src/'] +source_urls = ['https://gmsh.info/src/'] sources = ['%(name)s-%(version)s-source.tgz'] checksums = ['9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b'] diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb index c418370c84f..af7fa873717 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb @@ -4,13 +4,13 @@ name = 'gmsh' version = '3.0.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://geuz.org/gmsh' +homepage = 'https://gmsh.info/' description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {"usempi": True} -source_urls = ['http://gmsh.info/src/'] +source_urls = ['https://gmsh.info/src/'] sources = ['%(name)s-%(version)s-source.tgz'] checksums = ['9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b'] diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb index 9b05a009cb9..020cbc92d43 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb @@ -4,13 +4,13 @@ name = 'gmsh' version = '4.2.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://geuz.org/gmsh' +homepage = 'https://gmsh.info/' description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {"usempi": True} -source_urls = ['http://gmsh.info/src/'] +source_urls = ['https://gmsh.info/src/'] sources = ['%(name)s-%(version)s-source.tgz'] checksums = ['e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc'] From fc54e024e6d541684eda3ce811ff8e26707816b8 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 26 Apr 2020 23:04:18 +0200 Subject: [PATCH 216/431] adding easyconfigs: patchelf-0.10-GCCcore-8.3.0.eb --- .../p/patchelf/patchelf-0.10-GCCcore-8.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..665ffeeaade --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.10' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b3cb6bdedcef5607ce34a350cf0b182eb979f8f7bc31eae55a93a70a3f020d13'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From a75176a642a9c251117ad5448ff477a5de629fcd Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Mon, 27 Apr 2020 15:21:59 +1000 Subject: [PATCH 217/431] Create libffcall-2.2-GCCcore-8.3.0.eb --- .../libffcall/libffcall-2.2-GCCcore-8.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..b0e3541518b --- /dev/null +++ b/easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libffcall' +version = '2.2' + +homepage = 'https://www.gnu.org/software/libffcall/' + +description = """ + GNU Libffcall is a collection of four libraries which can be used to build + foreign function call interfaces in embedded interpreters +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ebfa37f97b6c94fac24ecf3193f9fc829517cf81aee9ac2d191af993d73cb747'] + +builddependencies = [ + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['include/avcall.h', 'include/callback.h', 'include/trampoline.h', + 'include/vacall.h', 'lib/libavcall.a', 'lib/libcallback.a', + 'lib/libtrampoline.a', 'lib/libvacall.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'lib' From 62e7d6fea1226c412328bd342dd38ed8b7d06193 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 10:30:28 +0200 Subject: [PATCH 218/431] [GCCcore/9.3.0] add UCX 1.8.0 as dep for OpenMPI 4.0.3 using in foss/2020a (+ easyconfig for libfabric 1.9.1) --- .../libfabric-1.9.1-GCCcore-9.3.0.eb | 45 ++++++++++++++++ .../o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb | 3 +- .../u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb | 52 +++++++++++++++++++ 3 files changed, 99 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e5dc095a7a0 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.9.1' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['765fdf71d99d179d89480c82271f62da5f186f61fe3907b1a450a63713312c6a'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('UCX', '1.8.0'), +] + +preconfigopts = "./autogen.sh && " + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb index 6426e2d34ca..a508d0b8b98 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb @@ -12,7 +12,8 @@ checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] dependencies = [ ('zlib', '1.2.11'), - ('hwloc', '2.2.0') + ('hwloc', '2.2.0'), + ('UCX', '1.8.0'), ] # disable MPI1 compatibility for now, see what breaks... diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e1135fb6623 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb @@ -0,0 +1,52 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.8.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.7.0_binutils_2.34_api_fix.patch', +] +checksums = [ + 'e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d', # ucx-1.8.0.tar.gz + 'c09ebe4d734d520ae23f56d95ba0b91e464a42ccbaf435675424515ebd3fa3a9', # UCX-1.7.0_binutils_2.34_api_fix.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +# Mellanox devices also need libmlxN-devel depending on the driver in use +# (see issue openucx/ucx#4883) +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.13'), +] + +preconfigopts = 'autoreconf && ' +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'lib' From 33fd136440926e0ac90727ceee31d6625e16736d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 10:45:24 +0200 Subject: [PATCH 219/431] {lib}[GCCcore/9.3.0] Mesa v20.0.2 + libGLU v9.0.1 (+ deps) --- .../g/gzip/gzip-1.10-GCCcore-9.3.0.eb | 24 ++++++ .../l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb | 45 ++++++++++++ .../l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb | 27 +++++++ .../l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb | 19 +++++ .../libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb | 28 +++++++ .../libunwind-1.3.1-GCCcore-9.3.0.eb | 32 ++++++++ .../l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb | 30 ++++++++ .../m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb | 27 +++++++ .../m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb | 73 +++++++++++++++++++ .../z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb | 41 +++++++++++ 10 files changed, 346 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..162b41ce551 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-9.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.10' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..65cd70d2417 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-9.0.1-GCCcore-9.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '9.0.1' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Python', '3.8.2'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' +build_type = 'Release' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..db58d867108 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.1' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Mesa', '20.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e7d1d72f50e --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.100-GCCcore-9.3.0.eb @@ -0,0 +1,19 @@ +name = 'libdrm' +version = '2.4.100' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6a5337c054c0c47bc16607a21efa2b622e08030be4101ef4a241c5eb05b6619b'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] +dependencies = [('X11', '20200222')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..26087064e8d --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libglvnd' +version = '1.2.0' + +homepage = 'https://github.com/NVIDIA/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/NVIDIA/libglvnd/releases/download/v%(version)s/'] +sources = ['libglvnd-%(version)s.tar.gz'] +checksums = ['2dacbcfa47b7ffb722cbddc0a4f1bc3ecd71d2d7bb461bceb8e396dc6b81dc6d'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('X11', '20200222')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..feb47934f25 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.3.1' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('XZ', '5.2.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4e7dff3111f --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-9.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.2' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['658ba6191fa44c92280d4aa2c271b0f4fbc0e34d249578dd05e50e76d0e5efcc'] + +builddependencies = [('binutils', '2.34')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..995c711c084 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.2-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.1.2' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3139c5d64aa5d175dbafb95027057128b5fbd05a40c53999f3905ceb53366d9d'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.34')] +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d1299b7b9a8 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb @@ -0,0 +1,73 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers are enabled based on system architecture: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# Default renderer is llvmpipe. SWR can be enabled by setting the environment +# variable GALLIUM_DRIVER=swr + +name = 'Mesa' +version = '20.0.2' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Mesa-%(version)s-match-swrast-loosely.patch'] +checksums = [ + 'aa54f1cb669550606aab8ceb475105d15aeb814fca5a778ce70d0fd10e98e86f', # mesa-20.0.2.tar.xz + 'e86abc2b9a9ad3e2fc604ad5d9bfe15a62e842e9900365fe7061849ea7438d90', # Mesa-20.0.2-match-swrast-loosely.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('pkg-config', '0.29.2'), + ('Mako', '1.1.2'), + ('libxml2', '2.9.10'), + ('expat', '2.2.9'), + ('gettext', '0.20.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('zstd', '1.4.4'), + ('libdrm', '2.4.100'), + ('libglvnd', '1.2.0'), + ('libunwind', '1.3.1'), + ('LLVM', '9.0.1'), + ('X11', '20200222'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=gallium -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d58083f3e5f --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.4.4-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.4.4' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a364f5162c7d1a455cc915e8e3cf5f4bd8b75d09bc0f53965b0c9ca1383c52c8'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('XZ', '5.2.5'), + ('lz4', '1.9.2'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From f8681f0c381ed36bb8b69e5698ecdf71a4b9dd35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 10:46:37 +0200 Subject: [PATCH 220/431] add missing patch file for UCX 1.8.0 --- .../UCX/UCX-1.7.0_binutils_2.34_api_fix.patch | 102 ++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch b/easybuild/easyconfigs/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch new file mode 100644 index 00000000000..8e7e359bbb3 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.7.0_binutils_2.34_api_fix.patch @@ -0,0 +1,102 @@ +commit 93bdcb84b707078431c8ddffbfd7a188173cc3f3 +Author: Sergey Oblomov +Date: Mon Mar 23 21:53:10 2020 +0200 + + BUILD/DEBUG: added new API of binutils + + - enables support of new API provided by binutils 2.34+ + +diff --git a/config/m4/ucs.m4 b/config/m4/ucs.m4 +index f329e50..6722a70 100644 +--- a/config/m4/ucs.m4 ++++ b/config/m4/ucs.m4 +@@ -43,6 +43,29 @@ AS_IF([test "x$enable_backtrace_detail" = xyes], + AC_CHECK_TYPES([struct dl_phdr_info], [], [AC_MSG_WARN([struct dl_phdr_info not defined])];BT=0, + [#define _GNU_SOURCE 1 + #include ]) ++ AC_CHECK_DECLS([bfd_get_section_flags, bfd_section_flags, bfd_get_section_vma, bfd_section_vma], ++ [], [], [#include ]) ++ ++ AC_MSG_CHECKING([bfd_section_size API version]) ++ AC_LANG_PUSH([C]) ++ SAVE_CFLAGS="$CFLAGS" ++ AC_COMPILE_IFELSE([AC_LANG_SOURCE([[ ++ #include ++ int main(int argc, char** argv) { ++ asection *sec = malloc(sizeof(*sec)); ++ bfd_section_size(sec); ++ free(sec); ++ return 0; ++ } ]])], ++ [AC_MSG_RESULT([1-arg API]) ++ AC_DEFINE([HAVE_1_ARG_BFD_SECTION_SIZE], [1], ++ [bfd_section_size 1-arg version])], ++ [AC_MSG_RESULT([2-args API]) ++ AC_DEFINE([HAVE_1_ARG_BFD_SECTION_SIZE], [0], ++ [bfd_section_size 2-args version])]) ++ CFLAGS="$SAVE_CFLAGS" ++ AC_LANG_POP([C]) ++ + if test "x$BT" = "x1"; then + AC_CHECK_FUNCS([cplus_demangle]) + AC_DEFINE([HAVE_DETAILED_BACKTRACE], 1, [Enable detailed backtrace]) +diff --git a/src/ucs/debug/debug.c b/src/ucs/debug/debug.c +index b5bd4a9..d7d6d46 100644 +--- a/src/ucs/debug/debug.c ++++ b/src/ucs/debug/debug.c +@@ -55,6 +55,34 @@ struct dl_address_search { + + #ifdef HAVE_DETAILED_BACKTRACE + ++#if HAVE_DECL_BFD_GET_SECTION_FLAGS ++# define ucs_debug_bfd_section_flags(_abfd, _section) \ ++ bfd_get_section_flags(_abfd, _section) ++#elif HAVE_DECL_BFD_SECTION_FLAGS ++# define ucs_debug_bfd_section_flags(_abfd, _section) \ ++ bfd_section_flags(_section) ++#else ++# error "Unsupported BFD API" ++#endif ++ ++#if HAVE_DECL_BFD_GET_SECTION_VMA ++# define ucs_debug_bfd_section_vma(_abfd, _section) \ ++ bfd_get_section_vma(_abfd, _section) ++#elif HAVE_DECL_BFD_SECTION_VMA ++# define ucs_debug_bfd_section_vma(_abfd, _section) \ ++ bfd_section_vma(_section) ++#else ++# error "Unsupported BFD API" ++#endif ++ ++#if HAVE_1_ARG_BFD_SECTION_SIZE ++# define ucs_debug_bfd_section_size(_abfd, _section) \ ++ bfd_section_size(_section) ++#else ++# define ucs_debug_bfd_section_size(_abfd, _section) \ ++ bfd_section_size(_abfd, _section); ++#endif ++ + struct backtrace_line { + unsigned long address; + char *file; +@@ -287,17 +315,17 @@ static void find_address_in_section(bfd *abfd, asection *section, void *data) + int found; + + if ((search->count > 0) || (search->max_lines == 0) || +- ((bfd_get_section_flags(abfd, section) & SEC_ALLOC) == 0)) { ++ ((ucs_debug_bfd_section_flags(abfd, section) & SEC_ALLOC) == 0)) { + return; + } + + address = search->file->dl.address - search->file->dl.base; +- vma = bfd_get_section_vma(abfd, section); ++ vma = ucs_debug_bfd_section_vma(abfd, section); + if (address < vma) { + return; + } + +- size = bfd_section_size(abfd, section); ++ size = ucs_debug_bfd_section_size(abfd, section); + if (address >= vma + size) { + return; + } From d95a82df15fcbf5231e15285748b3d7c52c445c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 11:01:17 +0200 Subject: [PATCH 221/431] add missing patch file for Mesa --- .../Mesa-20.0.2-match-swrast-loosely.patch | 84 +++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-match-swrast-loosely.patch diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-match-swrast-loosely.patch b/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-match-swrast-loosely.patch new file mode 100644 index 00000000000..cc36795634a --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-match-swrast-loosely.patch @@ -0,0 +1,84 @@ +# Fixes: swrast fails to load with certain remote X servers +# https://gitlab.freedesktop.org/mesa/mesa/issues/99 +# From Tom Hughes , June 2015 +# Adapted for later Mesa by Bart Oldeman , September 2019 +# Breaks "radeonsi" driver but this driver is not built by the easyconfig. +--- src/glx/dri_common.c.orig 2020-03-19 22:11:21.522610000 +0100 ++++ src/glx/dri_common.c 2020-03-19 22:14:39.290225004 +0100 +@@ -200,6 +200,36 @@ + } + + static int ++scalarGreaterEqual(struct glx_config *mode, unsigned int attrib, unsigned int value) ++{ ++ unsigned int glxValue; ++ int i; ++ ++ for (i = 0; i < ARRAY_SIZE(attribMap); i++) ++ if (attribMap[i].attrib == attrib) { ++ glxValue = *(unsigned int *) ((char *) mode + attribMap[i].offset); ++ return glxValue == GLX_DONT_CARE || glxValue >= value; ++ } ++ ++ return GL_TRUE; /* Is a non-existing attribute greater than or equal to value? */ ++} ++ ++static int ++booleanSupported(struct glx_config *mode, unsigned int attrib, unsigned int value) ++{ ++ unsigned int glxValue; ++ int i; ++ ++ for (i = 0; i < ARRAY_SIZE(attribMap); i++) ++ if (attribMap[i].attrib == attrib) { ++ glxValue = *(unsigned int *) ((char *) mode + attribMap[i].offset); ++ return glxValue == GLX_DONT_CARE || glxValue; ++ } ++ ++ return GL_TRUE; /* Is a non-existing attribute supported? */ ++} ++ ++static int + driConfigEqual(const __DRIcoreExtension *core, + struct glx_config *config, const __DRIconfig *driConfig) + { +@@ -247,7 +277,38 @@ + if (value & __DRI_ATTRIB_TEXTURE_RECTANGLE_BIT) + glxValue |= GLX_TEXTURE_RECTANGLE_BIT_EXT; + if (config->bindToTextureTargets != GLX_DONT_CARE && +- glxValue != config->bindToTextureTargets) ++ config->bindToTextureTargets && ++ glxValue != (config->bindToTextureTargets & glxValue)) ++ return GL_FALSE; ++ break; ++ ++ case __DRI_ATTRIB_STENCIL_SIZE: ++ case __DRI_ATTRIB_ACCUM_RED_SIZE: ++ case __DRI_ATTRIB_ACCUM_GREEN_SIZE: ++ case __DRI_ATTRIB_ACCUM_BLUE_SIZE: ++ case __DRI_ATTRIB_ACCUM_ALPHA_SIZE: ++ if (value != 0 && !scalarEqual(config, attrib, value)) ++ return GL_FALSE; ++ break; ++ ++ case __DRI_ATTRIB_DOUBLE_BUFFER: ++ case __DRI_ATTRIB_FRAMEBUFFER_SRGB_CAPABLE: ++ if (value && !booleanSupported(config, attrib, value)) ++ return GL_FALSE; ++ break; ++ ++ case __DRI_ATTRIB_BIND_TO_TEXTURE_RGB: ++ case __DRI_ATTRIB_BIND_TO_TEXTURE_RGBA: ++ case __DRI_ATTRIB_BIND_TO_MIPMAP_TEXTURE: ++ break; ++ ++ case __DRI_ATTRIB_SAMPLE_BUFFERS: ++ case __DRI_ATTRIB_SAMPLES: ++ case __DRI_ATTRIB_AUX_BUFFERS: ++ case __DRI_ATTRIB_MAX_PBUFFER_WIDTH: ++ case __DRI_ATTRIB_MAX_PBUFFER_HEIGHT: ++ case __DRI_ATTRIB_MAX_PBUFFER_PIXELS: ++ if (!scalarGreaterEqual(config, attrib, value)) + return GL_FALSE; + break; + From 839c8a603201cac9c4f4eae9d4e81c872da8007d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 11:31:17 +0200 Subject: [PATCH 222/431] rely on default sanity check performed by GoPackage easyblock --- easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb | 9 --------- easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb | 9 --------- 2 files changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb index 49597f83d08..6b52423375b 100644 --- a/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb +++ b/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb @@ -22,13 +22,4 @@ builddependencies = [ ('Go', '1.14'), ] -sanity_check_paths = { - 'files': ['bin/goalign'], - 'dirs': [], -} - -sanity_check_commands = [ - 'goalign --help' -] - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb b/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb index 2c870f187e7..cd860297c31 100644 --- a/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb +++ b/easybuild/easyconfigs/g/gotree/gotree-0.4.0.eb @@ -22,13 +22,4 @@ builddependencies = [ ('Go', '1.14'), ] -sanity_check_paths = { - 'files': ['bin/gotree'], - 'dirs': [], -} - -sanity_check_commands = [ - 'gotree --help' -] - moduleclass = 'bio' From ab29a11f54cf6cf5c5d687b645c588569cd2251e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 11:35:36 +0200 Subject: [PATCH 223/431] fix SHA256 checksum for goalign-0.3.2_go-mod.patch --- easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb index 6b52423375b..f9bc8deee9f 100644 --- a/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb +++ b/easybuild/easyconfigs/g/goalign/goalign-0.3.2.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] patches = [('%(name)s-%(version)s_go-mod.patch', 1)] checksums = [ 'e499889916eaaa6955f179e45870b06e862c6a90c6fc2a7d62d618e965e26c01', # v0.3.2.tar.gz - 'e055d77d901f4bc13cf32d010b2b44e28c07a764778dd0e8d752b482ed26165f', # goalign-0.3.2_go-mod.patch + '623c9662230e841bee492dc21fa764842f94941017fc1c7893260e739c62e0b3', # goalign-0.3.2_go-mod.patch ] builddependencies = [ From 4877577c4258350d8ea0729eb77e52be22a39780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 12:00:31 +0200 Subject: [PATCH 224/431] don't require custom sanity check for easyconfigs using GoPackage --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d7eae8d8f3a..2240c735bab 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -614,9 +614,10 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): def check_sanity_check_paths(self, changed_ecs): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" - # PythonBundle & PythonPackage already have a decent customised sanity_check_paths + # GoPackage, PythonBundle & PythonPackage already have a decent customised sanity_check_paths # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['CrayToolchain', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain', 'BuildEnv'] + whitelist = ['BuildEnv', 'CrayToolchain', 'GoPackage', 'ModuleRC', 'PythonBundle', 'PythonPackage', + 'Toolchain'] # Autotools & (recent) GCC are just bundles (Autotools: Autoconf+Automake+libtool, GCC: GCCcore+binutils) bundles_whitelist = ['Autotools', 'GCC'] From e4fb38aadbbbee2493b6adda1cd9afb9137fdf77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 12:04:28 +0200 Subject: [PATCH 225/431] {toolchain} intel/2020a --- .../easyconfigs/h/HPL/HPL-2.3-intel-2020a.eb | 21 ++++++++++ .../i/iccifort/iccifort-2020.1.217.eb | 40 +++++++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-2020a.eb | 18 +++++++++ .../i/imkl/imkl-2020.1.217-iimpi-2020a.eb | 39 ++++++++++++++++++ .../impi-2019.7.217-iccifort-2020.1.217.eb | 40 +++++++++++++++++++ easybuild/easyconfigs/i/intel/intel-2020a.eb | 21 ++++++++++ 6 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020a.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2020a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020a.eb new file mode 100644 index 00000000000..e671c6be5e7 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2020a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb new file mode 100644 index 00000000000..89d42319787 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'iccifort' +version = '2020.1.217' + +homepage = 'https://software.intel.com/en-us/intel-compilers/' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] +patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] +checksums = [ + # parallel_studio_xe_2020_update1_composer_edition.tgz + '26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', + # iccifort-2020.1.217_no_mpi_rt_dependency.patch + '61b558089d3d9253fad2139a16dc0899b9f839f34303e094efd70b281fc41a96', +] + +local_gccver = '9.3.0' + +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.34', '', ('GCCcore', local_gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = [ + 'intel-comp', 'intel-ccomp', 'intel-fcomp', 'intel-icc', 'intel-ifort', + 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' +] + +dontcreateinstalldir = True + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2020a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2020a.eb new file mode 100644 index 00000000000..4c30378af97 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2020a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2020a' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_compver = '2020.1.217' +dependencies = [ + ('iccifort', local_compver), + ('impi', '2019.7.217', '', ('iccifort', local_compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb new file mode 100644 index 00000000000..7f816072147 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpi-2020a.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.1.217' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb new file mode 100644 index 00000000000..d0ad0188c0d --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifort-2020.1.217.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.7.217' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] + +dependencies = [ + # needed by libfabric provider MLX introduced in Intel MPI v2019.6, + # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband + ('UCX', '1.8.0'), +] + +dontcreateinstalldir = True + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = True + +modextravars = { + # to enable SLURM integration with srun (site-specific) + # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', + + # set this if mpirun gives you a floating point exception (SIGFPE), see + # https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/852307 + # 'I_MPI_HYDRA_TOPOLIB': 'ipl', +} + +# may be needed if you enable I_MPI_PMI_LIBRARY above +# osdependencies = [('slurm-libpmi')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2020a.eb b/easybuild/easyconfigs/i/intel/intel-2020a.eb new file mode 100644 index 00000000000..99726a2e2be --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2020a.eb @@ -0,0 +1,21 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2020a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_compver = '2020.1.217' +local_gccver = '9.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.34', '', ('GCCcore', local_gccver)), + ('iccifort', local_compver), + ('impi', '2019.7.217', '', ('iccifort', local_compver)), + ('imkl', local_compver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 28cde65fc6c849ba98b25faffe74849bfa96c1bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 12:08:11 +0200 Subject: [PATCH 226/431] add patch for iccifirt 2020.1.217 --- .../iccifort-2020.1.217_no_mpi_rt_dependency.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch new file mode 100644 index 00000000000..65900e15cbd --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2020.1.217_no_mpi_rt_dependency.patch @@ -0,0 +1,13 @@ +don't install Intel MPI runtime components (mpi-rt), cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/3793 +author: Bart Oldeman (Compute Canada), updated for 2020.1.217 by Kenneth Hoste (HPC-UGent) +--- parallel_studio_xe_2020_update1_composer_edition/pset/mediaconfig.xml.orig 2020-03-31 17:31:11.362126388 +0200 ++++ parallel_studio_xe_2020_update1_composer_edition/pset/mediaconfig.xml 2020-03-31 17:31:30.691960582 +0200 +@@ -870,7 +870,7 @@ + + ${COMPLIB_ROOT} + 1585047222050 +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel Fortran Compiler 19.1 Update 1 + インテル(R) Fortran コンパイラー (インテル(R) 64) From f5501dd498dc0ed9123f31e47ee95aa1fbf576ef Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Mon, 27 Apr 2020 13:09:21 +0200 Subject: [PATCH 227/431] adding easyconfigs: protozero-1.6.8-GCCcore-7.3.0.eb --- .../protozero-1.6.8-GCCcore-7.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/protozero/protozero-1.6.8-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/p/protozero/protozero-1.6.8-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/protozero/protozero-1.6.8-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..2abf8a91f9c --- /dev/null +++ b/easybuild/easyconfigs/p/protozero/protozero-1.6.8-GCCcore-7.3.0.eb @@ -0,0 +1,27 @@ +easyblock = "CMakeMake" + +name = 'protozero' +version = '1.6.8' + +homepage = "https://github.com/mapbox/protozero" +description = "Minimalistic protocol buffer decoder and encoder in C++." + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/mapbox/protozero/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['019a0f3789ad29d7e717cf2e0a7475b36dc180508867fb47e8c519885b431706'] + +builddependencies = { + ('CMake', '3.12.1'), + ('binutils', '2.30'), +} + +sanity_check_paths = { + 'files': ['include/protozero/%s.hpp' % x for x in ['byteswap', 'config', 'data_view', 'exception', 'iterators', + 'pbf_builder', 'pbf_message', 'pbf_reader', 'pbf_writer', + 'types', 'varint', 'version']], + 'dirs': ['include/protozero'] +} + +moduleclass = "devel" From 3c7213e94cccd3fbba542acfc0f847903c1655ee Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 27 Apr 2020 13:42:39 +0200 Subject: [PATCH 228/431] [OTF2 & Score-P] Move builddependencies to dependencies As discussed in https://github.com/easybuilders/easybuild-easyconfigs/pull/10397#issuecomment-619363052 those should be runtime dependencies as they are used at runtime --- easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb | 2 ++ easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb | 2 ++ easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019a.eb | 7 +------ 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb index f710d39d2d9..6fa20d819fa 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb @@ -33,6 +33,8 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.31.1'), +] +dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.4', '-tools'), ] diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb index 2e6c29be6c4..4c77f62f44d 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb @@ -33,6 +33,8 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.32'), +] +dependencies = [ # SIONlib container support (optional): ('SIONlib', '1.7.6', '-tools'), ] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019a.eb index 3dfd35f063c..dc46844f25e 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019a.eb @@ -27,16 +27,11 @@ checksums = [ '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz ] -builddependencies = [ +dependencies = [ ('CubeLib', '4.4.4'), ('CubeWriter', '4.4.3'), # Unwinding/sampling support (optional): ('libunwind', '1.3.1'), -] - -dependencies = [ - # binutils is implicitly available via GCC toolchain - # ('binutils', '2.31.1'), ('OPARI2', '2.0.5'), ('OTF2', '2.2'), # Hardware counter support (optional): From 021bda9ff29b360e84fd1e5c24a860765775443d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 14:55:19 +0200 Subject: [PATCH 229/431] {lib}[GCCcore/9.3.0] Qt5 v5.14.1 (+ deps) --- .../d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb | 42 +++++++++++++ .../double-conversion-3.1.5-GCCcore-9.3.0.eb | 38 ++++++++++++ .../g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb | 52 ++++++++++++++++ .../j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb | 35 +++++++++++ .../libevent/libevent-2.1.11-GCCcore-9.3.0.eb | 37 +++++++++++ .../libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb | 42 +++++++++++++ .../n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb | 37 +++++++++++ .../n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb | 28 +++++++++ .../n/NSS/NSS-3.51-GCCcore-9.3.0.eb | 49 +++++++++++++++ .../p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb | 45 ++++++++++++++ .../p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb | 28 +++++++++ .../q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb | 62 +++++++++++++++++++ .../r/re2c/re2c-1.3-GCCcore-9.3.0.eb | 25 ++++++++ .../s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb | 29 +++++++++ 14 files changed, 549 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/r/re2c/re2c-1.3-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..60227ab40fc --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.12-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.13.12' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7588649b56dd257c6a5f85a8c45aa2dfdf9e99f4de3983710f452081ca43eca6'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), +] + +configopts = '--without-systemdsystemunitdir' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..54a669f1a95 --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.1.5' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a63ecb93182134ba4293fd5f22d6e08ca417caafa244afaa751cbfddf6415b13'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..544f298af6b --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.64.1-GCCcore-9.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.64.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['17967603bcb44b6dbaac47988d80c29a3d28519210b28157c2bd10997595bbc7'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.8.2'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libffi', '3.3'), + ('gettext', '0.20.1'), + ('libxml2', '2.9.10'), + ('PCRE', '8.44'), + ('util-linux', '2.35'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c35a612e4a1 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.14' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.ece.uvic.ca/~frodo/jasper/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +separate_build_dir = True + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..46b3823d2dc --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.11-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.11' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['a65bac6202ea8c5609fd5c7e480e6d25de467ea1917c08290c521752f147283d'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e98cd35c5d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.4-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.0.4' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('binutils', '2.34'), +] + +dependencies = [ + ('NASM', '2.14.02'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4ab7a9fc7ab --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.14.02' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] + +builddependencies = [ + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8cfc285f74d --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.25-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.25' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://archive.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0bc309be21f91da4474c56df90415101c7f0c7c7cab2943cd943cd7896985256'] + +builddependencies = [('binutils', '2.34')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..39120284851 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.51' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', +] +checksums = [ + '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz + '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch +] + +builddependencies = [('binutils', '2.34')] +dependencies = [ + ('NSPR', '4.25'), + ('zlib', '1.2.11'), +] + +# building in parallel fails +parallel = 1 + +# fix for not being able to find header files +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['lib/libnss.a'], + 'dirs': ['bin', 'include/dbm', 'include/nss'], +} + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cdb3f57b911 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-9.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.44' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aecafd4af3bd0f3935721af77b889d9024b2e01d96b58471bd91a3063fb47728'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..964495dcb0e --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.34' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.sourceforge.net/pcre'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['da6aba7ba2509e918e41f4f744a59fa41a2425c59a298a232e7fe85691e00379'] + +builddependencies = [('binutils', '2.34')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..05c2a6c405c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.14.1' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', +] +checksums = [ + '6f17f488f512b39c2feb57d83a5e0a13dcef32999bea2e2a8f832f54a29badb8', # qt-everywhere-src-5.14.1.tar.xz + '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch + '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), + # deps for QtWebEngine + ('Bison', '3.5.3'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.0'), + ('Python', '3.8.2'), + ('re2c', '1.3') +] + +dependencies = [ + ('double-conversion', '3.1.5'), + ('GLib', '2.64.1'), + ('PCRE2', '10.34'), + ('libpng', '1.6.37'), + # deps for QtWebEngine + ('X11', '20200222'), + ('DBus', '1.13.12'), + ('libevent', '2.1.11'), + ('libGLU', '9.0.1'), + ('libjpeg-turbo', '2.0.4'), + ('NSS', '3.51'), + ('snappy', '1.1.8'), + ('JasPer', '2.0.14'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/re2c/re2c-1.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/r/re2c/re2c-1.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d7ce53e3165 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-1.3-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '1.3' + +homepage = 'https://re2c.org/' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['f37f25ff760e90088e7d03d1232002c2c2672646d5844fdf8e0d51a5cd75a503'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..bf652cb387d --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.8' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['16b677f07832a612b0836178db7f374e414f94657c138e6993cbfc5dcc58651f'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +configopts = ['', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [''] +} + +moduleclass = 'lib' From 9e24c75c81160b763e83326db51d8e8b04619564 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 15:31:58 +0200 Subject: [PATCH 230/431] make sure right Python version is picked up in old gmsh easyconfig --- .../g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb index c3bfdf84a6a..0f3e4ce5af9 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb @@ -19,15 +19,17 @@ builddependencies = [ ('SWIG', '3.0.12', versionsuffix), ] +local_pymajmin = '2.7' dependencies = [ - ('Python', '2.7.14'), + ('Python', local_pymajmin + '.14'), ('PETSc', '3.8.3', '-downloaded-deps'), ('SLEPc', '3.8.3'), ] separate_build_dir = True -configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1 ' +configopts += "-DPython_ADDITIONAL_VERSIONS='%s'" % local_pymajmin modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From 1574b0801c15ee97b9b9157637e7b179aae2bf6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 15:34:32 +0200 Subject: [PATCH 231/431] add missing patch file for NSS --- .../n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch b/easybuild/easyconfigs/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch new file mode 100644 index 00000000000..56e2edda9b1 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.51_fix_kremlin_ppc64le.patch @@ -0,0 +1,28 @@ +Patch based on https://github.com/FStarLang/kremlin/pull/167 +Prepared for EasyBuild by Simon Branford of the BEAR Software team at the University of Birmingham +diff -aur nss-3.51.orig/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h nss-3.51/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h +--- nss-3.51.orig/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h 2020-03-23 20:23:06.943356000 +0000 ++++ nss-3.51/nss/lib/freebl/verified/kremlin/include/kremlin/internal/types.h 2020-03-23 20:24:27.270377000 +0000 +@@ -56,7 +56,8 @@ + #include + typedef __m128i FStar_UInt128_uint128; + #elif !defined(KRML_VERIFIED_UINT128) && !defined(_MSC_VER) && \ +- (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__)) ++ (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__) || \ ++ (defined(__powerpc64__) && defined(__LITTLE_ENDIAN__))) + typedef unsigned __int128 FStar_UInt128_uint128; + #else + typedef struct FStar_UInt128_uint128_s { +diff -aur nss-3.51.orig/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h nss-3.51/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h +--- nss-3.51.orig/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h 2020-03-23 20:23:06.947505000 +0000 ++++ nss-3.51/nss/lib/freebl/verified/kremlin/kremlib/dist/minimal/fstar_uint128_gcc64.h 2020-03-23 20:25:20.007003000 +0000 +@@ -25,7 +25,8 @@ + #include "LowStar_Endianness.h" + + #if !defined(KRML_VERIFIED_UINT128) && !defined(_MSC_VER) && \ +- (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__)) ++ (defined(__x86_64__) || defined(__x86_64) || defined(__aarch64__) || \ ++ (defined(__powerpc64__) && defined(__LITTLE_ENDIAN__))) + + /* GCC + using native unsigned __int128 support */ + From bf8c2abdc6bb50d244cb8297c7728034620c6f41 Mon Sep 17 00:00:00 2001 From: jhein32 Date: Mon, 27 Apr 2020 15:39:24 +0200 Subject: [PATCH 232/431] white space I think you want to remove the white space in line 31, as I am now trying. This way that line shouldn't pop up as changed, which it actually isn't. --- .../easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb index 0f3e4ce5af9..3aad8cca108 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb @@ -28,7 +28,7 @@ dependencies = [ separate_build_dir = True -configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1 ' +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' configopts += "-DPython_ADDITIONAL_VERSIONS='%s'" % local_pymajmin modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From cb884d2111c2586b80afe5598f16a3d7790ee24e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 15:44:11 +0200 Subject: [PATCH 233/431] add patch for UCX 1.8.0 to fix unresolved symbol (see https://github.com/openucx/ucx/issues/4883) --- .../u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb | 4 +++ .../UCX/UCX-1.8.0_fix-undefined-symbol.patch | 30 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb index e1135fb6623..4de436a8cc4 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb @@ -18,10 +18,12 @@ source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ 'UCX-1.7.0_binutils_2.34_api_fix.patch', + 'UCX-1.8.0_fix-undefined-symbol.patch', ] checksums = [ 'e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d', # ucx-1.8.0.tar.gz 'c09ebe4d734d520ae23f56d95ba0b91e464a42ccbaf435675424515ebd3fa3a9', # UCX-1.7.0_binutils_2.34_api_fix.patch + 'eb757242ab3eecd8a851f329cb4baf3c64d46788ab61675f29ab4cc6a0274a45', # UCX-1.8.0_fix-undefined-symbol.patch ] builddependencies = [ @@ -49,4 +51,6 @@ sanity_check_paths = { 'dirs': ['include', 'lib', 'share'] } +sanity_check_commands = ["ucx_info -d"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch b/easybuild/easyconfigs/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch new file mode 100644 index 00000000000..2778984e3ff --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0_fix-undefined-symbol.patch @@ -0,0 +1,30 @@ +fix for "libuct_ib.so.0: undefined symbol: uct_ib_exp_qp_fill_attr" + +see https://github.com/openucx/ucx/issues/4883 + https://github.com/openucx/ucx/pull/4900 + +From 40d6991eca6b36c6bc2c557dccfbad7a48ce5f62 Mon Sep 17 00:00:00 2001 +From: Artemy Kovalyov +Date: Tue, 17 Mar 2020 13:34:19 +0200 +Subject: [PATCH] UCT/IB/MLX5: Fix EXP accel compilation + +--- + src/uct/ib/mlx5/exp/ib_exp.h | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/src/uct/ib/mlx5/exp/ib_exp.h b/src/uct/ib/mlx5/exp/ib_exp.h +index ab1d9237e1..e97f574b17 100644 +--- a/src/uct/ib/mlx5/exp/ib_exp.h ++++ b/src/uct/ib/mlx5/exp/ib_exp.h +@@ -7,7 +7,11 @@ + #ifndef UCT_IB_MLX5_EXP_H_ + #define UCT_IB_MLX5_EXP_H_ + +-#if HAVE_VERBS_EXP_H ++#ifdef HAVE_CONFIG_H ++# include "config.h" ++#endif ++ ++#if HAVE_MLX5_HW && HAVE_VERBS_EXP_H + void uct_ib_exp_qp_fill_attr(uct_ib_iface_t *iface, uct_ib_qp_attr_t *attr); + #else + static inline void uct_ib_exp_qp_fill_attr(uct_ib_iface_t *iface, uct_ib_qp_attr_t *attr) { } From be28a421423a4f3dc9a151659e544b36bc26aed0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 15:49:29 +0200 Subject: [PATCH 234/431] drop comment from UCX 1.8.0 easyconfig that is now irrelevant, issue fixed with patch --- easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb index 4de436a8cc4..e029f5e98cc 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb @@ -32,8 +32,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -# Mellanox devices also need libmlxN-devel depending on the driver in use -# (see issue openucx/ucx#4883) osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ From 9b5324fdfc344deb59202766ccc8ff65d9d9636e Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 27 Apr 2020 15:51:21 +0200 Subject: [PATCH 235/431] Re-established whitespace in gmsh-3.0.6-foss-2017b-Python-2.7.14.eb Change done on Kenneth' recommendation --- .../easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb index 3aad8cca108..0f3e4ce5af9 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2017b-Python-2.7.14.eb @@ -28,7 +28,7 @@ dependencies = [ separate_build_dir = True -configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1 ' configopts += "-DPython_ADDITIONAL_VERSIONS='%s'" % local_pymajmin modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From b066088f91acf428de2cc597f6d1915f35d68c4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 16:58:29 +0200 Subject: [PATCH 236/431] {lang,vis}[foss/2020a,intel/2020a] SciPy-bundle v2020.03 + matplotlib v3.2.1 --- .../e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb | 24 ++++++++ ...atplotlib-3.2.1-foss-2020a-Python-3.8.2.eb | 57 ++++++++++++++++++ ...tplotlib-3.2.1-intel-2020a-Python-3.8.2.eb | 58 +++++++++++++++++++ ...bind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb | 33 +++++++++++ ...-bundle-2020.03-foss-2020a-Python-3.8.2.eb | 51 ++++++++++++++++ ...bundle-2020.03-intel-2020a-Python-3.8.2.eb | 55 ++++++++++++++++++ .../t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb | 40 +++++++++++++ .../t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb | 25 ++++++++ 8 files changed, 343 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f8845744a0a --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-9.3.0.eb @@ -0,0 +1,24 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Eigen' +version = '3.3.7' + +homepage = 'https://eigen.tuxfamily.org/index.php?title=Main_Page' + +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['685adf14bd8e9c015b78097c1dc22f2f01343756f196acdc76a678e1ae352e11'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.34'), # to make CMake compiler health check pass on old systems + ('CMake', '3.16.4'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..b57ab849cd6 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..9b8d59a1fb2 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.2.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +check_ldshared = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..e43f10744da --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'pybind11' +version = '2.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Eigen', '3.3.7'), +] +dependencies = [ + ('Python', '3.8.2'), +] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/pybind11', 'share/cmake/pybind11'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..274cf739c55 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.03' +versionsuffix = '-Python-3.8.2' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.2'), + ('pybind11', '2.4.3', versionsuffix), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.18.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8'], + }), + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('pandas', '1.0.3', { + 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..d6689ded6e4 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.03' +versionsuffix = '-Python-3.8.2' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.2'), + ('pybind11', '2.4.3', versionsuffix), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.18.3', { + 'patches': ['numpy-1.18.2-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.2.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + ], + }), + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('pandas', '1.0.3', { + 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cadac1ca545 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-9.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '63df418a859d0a463347f95ded5cd88a3dd3aaa1ceecaeee362194bc30f3e386', # tk8.6.10-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.34')] +dependencies = [ + ('Tcl', version), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e14f4742215 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.2-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.8.2' + +homepage = 'https://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561'] + +builddependencies = [ + ('binutils', '2.34'), + ('libffi', '3.3'), +] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.10'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From 143ec42d89ffa28c79ac71143e46fc61284dd977 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 17:14:59 +0200 Subject: [PATCH 237/431] add missing patch files for numpy & scipy in SciPy-bundle 2020.03 --- .../s/SciPy-bundle/numpy-1.18.2-mkl.patch | 57 +++++++++++++++++++ .../scipy-1.4.1-fix-pthread.patch | 39 +++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.18.2-mkl.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.18.2-mkl.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.18.2-mkl.patch new file mode 100644 index 00000000000..ca3df86ffe2 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.18.2-mkl.patch @@ -0,0 +1,57 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) + +Remade against numpy-1.18.2, 20200317, Åke Sandgren (HPC2N) +diff -ru numpy-1.18.2.orig/numpy/distutils/fcompiler/__init__.py numpy-1.18.2/numpy/distutils/fcompiler/__init__.py +--- numpy-1.18.2.orig/numpy/distutils/fcompiler/__init__.py 2020-03-09 17:18:24.000000000 +0100 ++++ numpy-1.18.2/numpy/distutils/fcompiler/__init__.py 2020-03-17 20:05:39.284278141 +0100 +@@ -637,7 +637,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.18.2.orig/numpy/distutils/system_info.py numpy-1.18.2/numpy/distutils/system_info.py +--- numpy-1.18.2.orig/numpy/distutils/system_info.py 2020-03-09 17:18:24.000000000 +0100 ++++ numpy-1.18.2/numpy/distutils/system_info.py 2020-03-17 20:05:39.284278141 +0100 +@@ -831,7 +831,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -918,6 +918,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.18.2.orig/numpy/distutils/unixccompiler.py numpy-1.18.2/numpy/distutils/unixccompiler.py +--- numpy-1.18.2.orig/numpy/distutils/unixccompiler.py 2020-03-09 17:18:24.000000000 +0100 ++++ numpy-1.18.2/numpy/distutils/unixccompiler.py 2020-03-17 20:05:39.284278141 +0100 +@@ -137,3 +137,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch new file mode 100644 index 00000000000..d399b2ba412 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.4.1-fix-pthread.patch @@ -0,0 +1,39 @@ +From https://github.com/scipy/scipy/pull/11324 +Author: Peter Bell +diff --git a/scipy/fft/_pocketfft/setup.py b/scipy/fft/_pocketfft/setup.py +index a4411bdedb1..493387d9719 100644 +--- a/scipy/fft/_pocketfft/setup.py ++++ b/scipy/fft/_pocketfft/setup.py +@@ -5,20 +5,28 @@ def pre_build_hook(build_ext, ext): + cc = build_ext._cxx_compiler + args = ext.extra_compile_args + +- std_flag = get_cxx_std_flag(build_ext._cxx_compiler) ++ std_flag = get_cxx_std_flag(cc) + if std_flag is not None: + args.append(std_flag) + + if cc.compiler_type == 'msvc': + args.append('/EHsc') + else: +- try_add_flag(args, cc, '-fvisibility=hidden') +- ++ # Use pthreads if available + has_pthreads = try_compile(cc, code='#include \n' + 'int main(int argc, char **argv) {}') + if has_pthreads: + ext.define_macros.append(('POCKETFFT_PTHREADS', None)) +- ++ if has_flag(cc, '-pthread'): ++ args.append('-pthread') ++ ext.extra_link_args.append('-pthread') ++ else: ++ raise RuntimeError("Build failed: System has pthreads header " ++ "but could not compile with -pthread option") ++ ++ # Don't export library symbols ++ try_add_flag(args, cc, '-fvisibility=hidden') ++ # Set min macOS version + min_macos_flag = '-mmacosx-version-min=10.9' + import sys + if sys.platform == 'darwin' and has_flag(cc, min_macos_flag): From 48bc3387d905c647f372a96a076d2617768b881c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 17:55:37 +0200 Subject: [PATCH 238/431] adding easyconfigs: PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb --- ...Wavelets-1.1.1-intel-2019b-Python-3.7.4.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..a9fe93659b2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # for numpy +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' From 14852846c242850ba193e7dfaaa18f84f2b301ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 18:12:54 +0200 Subject: [PATCH 239/431] update to swissknife 1.80 for metaerg --- .../m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb | 2 +- ...9-GCCcore-8.3.0.eb => swissknife-1.80-GCCcore-8.3.0.eb} | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/s/swissknife/{swissknife-1.79-GCCcore-8.3.0.eb => swissknife-1.80-GCCcore-8.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb index 21a4673613d..215bbe4be6b 100644 --- a/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/metaerg/metaerg-1.2.3-intel-2019b-Python-2.7.16.eb @@ -32,7 +32,7 @@ dependencies = [ ('prodigal', '2.6.3'), ('MinCED', '0.4.2', '-Java-11'), ('Bio-EUtilities', '1.76'), - ('swissknife', '1.79'), + ('swissknife', '1.80'), ] modextrapaths = { diff --git a/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb similarity index 75% rename from easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb index f79876cb5ce..b6326ee5ebb 100644 --- a/easybuild/easyconfigs/s/swissknife/swissknife-1.79-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb @@ -4,17 +4,16 @@ easyblock = 'PerlModule' name = 'swissknife' -version = '1.79' +version = '1.80' homepage = 'https://sourceforge.net/projects/swissknife/' description = "Perl module for reading and writing UniProtKB data in plain text format." toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [('https://sourceforge.net/projects/swissknife/files/swissknife/1.79', 'download')] +source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['a7affa6ed892a8d9f4f9f1297d521076ac5bb1adfd85de5dc041679b53b949d6'] - +checksums = ['4e0bcf847ab658b6d59306ff362c63aec508a05503cd32a5c13ee51c7c22bc18'] builddependencies = [('binutils', '2.32')] dependencies = [ From 3de2a91856ca7e3d01a6ae1f06491c9ca23db3c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 18:44:23 +0200 Subject: [PATCH 240/431] remove broken test in swissknife 1.80 easyconfig --- .../easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb b/easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb index b6326ee5ebb..ea33c794c48 100644 --- a/easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/s/swissknife/swissknife-1.80-GCCcore-8.3.0.eb @@ -20,6 +20,8 @@ dependencies = [ ('Perl', '5.30.0'), ] +# remove broken tests, randomly fails due to different order in generated output file 'annot.txl.out' +pretestopts = "rm t/annot.t && " runtest = "test TEST_VERBOSE=1" options = {'modulename': 'SWISS::Entry'} From 8727547ed6901c07e6be97ada052414e6c751dd5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 29 Mar 2020 18:35:02 +0200 Subject: [PATCH 241/431] libfabric v1.9.1: add system dependencies on ibverbs and remove UCX --- .../easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb index e5dc095a7a0..167290b2bad 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.9.1-GCCcore-9.3.0.eb @@ -25,9 +25,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -dependencies = [ - ('UCX', '1.8.0'), -] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] preconfigopts = "./autogen.sh && " From 75d7e13b750e26e4e8eaa1697831dfc82e4eaa41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Apr 2020 20:48:57 +0200 Subject: [PATCH 242/431] adding easyconfigs: RNA-Bloom-1.2.3-GCC-8.3.0.eb, minimap2-2.17-GCC-8.3.0.eb, ntCard-1.2.1-GCC-8.3.0.eb --- .../m/minimap2/minimap2-2.17-GCC-8.3.0.eb | 40 +++++++++++++++++++ .../n/ntCard/ntCard-1.2.1-GCC-8.3.0.eb | 32 +++++++++++++++ .../r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb | 31 ++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.3.0.eb new file mode 100644 index 00000000000..fbcd8560699 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCC-8.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.17' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-8.3.0.eb b/easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-8.3.0.eb new file mode 100644 index 00000000000..86b1145102a --- /dev/null +++ b/easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-8.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ntCard' +version = '1.2.1' + +homepage = 'https://www.bcgsc.ca/resources/software/ntcard' +description = "ntCard is a streaming algorithm for estimating the frequencies of k-mers in genomics datasets." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d635dec6e293780a5ae2b7bb422ff5cc825a03270b507f5061cbf0f09ee7076'] + +builddependencies = [ + ('Autotools', '20180311'), +] + +# ignore "type qualifiers ignored on cast result type" warning being treated as error due to -Werror +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -Wno-ignored-qualifiers" && ' + +sanity_check_paths = { + 'files': ['bin/ntcard', 'bin/nthll'], + 'dirs': ['share/doc/ntcard'], +} + +sanity_check_commands = [ + "ntcard --help", + "nthll --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb new file mode 100644 index 00000000000..930af7a4bdc --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'RNA-Bloom' +version = '1.2.3' + +homepage = 'https://github.com/bcgsc/RNA-Bloom' +description = "RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/v1.2.3'] +sources = ['rnabloom_v1.2.3.tar.gz'] +checksums = ['7418761ff99f24f0edc23772cfa517c3d7401eac98642dcb017d48fb35c6ee4a'] + +dependencies = [ + ('Java', '1.8', '', True), + ('minimap2', '2.17'), + ('Racon', '1.4.13'), + ('ntCard', '1.2.1'), +] + +sanity_check_paths = { + 'files': ['LICENSE', 'README.md', 'rnabloom', 'RNA-Bloom.jar'], + 'dirs': [], +} + +sanity_check_commands = ["rnabloom --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From fd80ac651fa3c3a7745deb9d2e585076f53183c4 Mon Sep 17 00:00:00 2001 From: Jordi Blasco Pallares Date: Tue, 28 Apr 2020 18:27:09 +1200 Subject: [PATCH 243/431] Update easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb index a074a1a0ba1..3f88a35af9b 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.2.0-gompi-2019b.eb @@ -31,6 +31,8 @@ builddependencies = [ ('pkg-config', '0.29.2'), ('jemalloc', '5.2.1'), ('Boost', '1.71.0'), + ('cURL', '7.66.0'), + ('XZ', '5.2.4'), ('zlib', '1.2.11'), ('bzip2', '1.0.8'), ] From 7810d39955c5b186aea667952374faaff8fe9281 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 09:43:34 +0200 Subject: [PATCH 244/431] adding easyconfigs: FFTW-3.3.8-intel-2020a.eb --- .../f/FFTW/FFTW-3.3.8-intel-2020a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020a.eb new file mode 100644 index 00000000000..251e1c76c19 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2020a.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From d8e91ce76dc5cbc78df66f5f60fd223636014ca2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 09:53:29 +0200 Subject: [PATCH 245/431] {lang}[foss/2020a] R v3.6.3 (+ deps) --- .../c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb | 47 + .../easyconfigs/g/GSL/GSL-2.6-GCC-9.3.0.eb | 25 + .../Ghostscript-9.52-GCCcore-9.3.0.eb | 55 + .../i/ICU/ICU-66.1-GCCcore-9.3.0.eb | 29 + .../ImageMagick-7.0.10-1-GCCcore-9.3.0.eb | 44 + .../l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 42 + .../LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb | 29 + .../libsndfile-1.0.28-GCCcore-9.3.0.eb | 25 + .../n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb | 38 + .../p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb | 29 + .../easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 2332 +++++++++++++++++ .../u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb | 41 + 12 files changed, 2736 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..3a05c32e92b --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-9.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('pixman', '0.38.4'), + ('expat', '2.2.9'), + ('GLib', '2.64.1'), + ('X11', '20200222'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-9.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-9.3.0.eb new file mode 100644 index 00000000000..0311d9f4790 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-GCC-9.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a6bd2e9bd46 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.52' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c2501d8e8e0814c4a5aa7e443e230e73d7af7f70287546f7b697e5ef49e32176'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('libjpeg-turbo', '2.0.4'), + ('expat', '2.2.9'), + ('GLib', '2.64.1'), + ('cairo', '1.16.0'), + ('LibTIFF', '4.1.0'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.34'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c0e823ba2a7 --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '66.1' + +homepage = 'http://icu-project.org/' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['52a3f2209ab95559c1cf0a14f24338001f389615bf00e2585ef3dbc43ecf0a2e'] + +builddependencies = [ + ('binutils', '2.34'), + ('Python', '3.8.2'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0d6ab6b1978 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.10-1' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['61fcd748d3c3962c614c2df2645cf09ba7ae95b495cb27148dd5d2a8fc995713'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20200222'), + ('Ghostscript', '9.52'), + ('JasPer', '2.0.14'), + ('libjpeg-turbo', '2.0.4'), + ('LibTIFF', '4.1.0'), + ('LittleCMS', '2.9'), +] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e147e84dac0 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.1.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'https://download.osgeo.org/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.4') +] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f02cf0fcf1b --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.9' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['48c6fdf98396fa245ed86e622028caf49b96fa22f3e5734f853f806fbc8e7d20'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.34'), +] + +dependencies = [('libjpeg-turbo', '2.0.4')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b4b2d7c0047 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.28' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] + +builddependencies = [('binutils', '2.34')] + +configopts = '--enable-octave=no' + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..578a181a5fe --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2019-06-05 John Dey jfdey@fredhutch.org fizwit@github.com - updated for CMake +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.6.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['66d63a505187fb6f98642703bd0ef006fedcae2f9a6d1efa4f362ea919a02650'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('binutils', '2.34'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..93fcba8ecbc --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.4-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.38.4' + +homepage = 'http://www.pixman.org/' + +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['da66d6fd6e40aee70f7bd02e4f8f76fc3f006ec879d346bae6a723025cfbdde7'] + +builddependencies = [ + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb new file mode 100644 index 00000000000..a59f35b2183 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -0,0 +1,2332 @@ +name = 'R' +version = '3.6.3' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', '20200222'), + ('Mesa', '20.0.2'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.31.1'), + ('PCRE', '8.44'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.4'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.69.1'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.1'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '66.1'), # for rJava & gdsfmt + ('HDF5', '1.10.6'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-1'), # for animation + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1e'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 25 March 2020 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.4', { + 'checksums': ['d992fe8f7480606a0790be94948a6b667f37aa607ccd5e5613e88af861bb00d5'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '1.1-15.2', { + 'checksums': ['0b83e78385293d6cdc0189a07fcc3f9f9db286c8c4af3288467f5257e79cb28b'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '2.2-14', { + 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], + }), + ('bnlearn', '4.5', { + 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], + 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['0b1183458d625ef5dd0962fc77ca1326e77754a2c04be11fb002057abcb65a22'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-57', { + 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-8', { + 'checksums': ['4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.4', { + 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.8', { + 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '2.1', { + 'checksums': ['d21959ce5b1ee20efd1483f6020b57e5f6616bd525af77a7bd325501cc670606'], + }), + ('bbmle', '1.0.23.1', { + 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.47', { + 'checksums': ['123ebe870895c2ba3a4b64d8a18bccab5287c831fa14bb0fe07f0d7de61e51d3'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2020.03.16', { + 'checksums': ['160eb4ea23be53305e4e728002c8f5d3852d89155f538deccb734e7c8ad4e1c3'], + }), + ('stopwords', '1.0', { + 'checksums': ['9b727a5d827ac8dcfa6329140d294dcf964a06d80132b4ca434330d0ee02b1da'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.6.0', { + 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0', { + 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], + }), + ('topicmodels', '0.2-9', { + 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], + }), + ('tidytext', '0.2.3', { + 'checksums': ['c103f98f5cbbb5a4ea4c893520ea5eb38b9c5097e5325d7efd4f7e3afe71068b'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-1', { + 'checksums': ['520ef83e9a7c58e3c5b7175fbda902b747b2e01c24b53714ede81a6a87de5b64'], + }), + ('loo', '2.2.0', { + 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'], + }), + ('StanHeaders', '2.21.0-1', { + 'checksums': ['4e94148af2960f203b208c2b725d8be628ca282c7a1e967a7e6e78aa5eb90d3f'], + }), + ('rstan', '2.19.3', { + 'checksums': ['d7025dccdc2337fd0cf3b9689c3e0a07558a47a08b7cbc370e0b3998256f1689'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..fc005b2533e --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('expat', '2.2.9')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 2eefde59a5922bd767ade0c58c7617e26ff5a551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 10:12:32 +0200 Subject: [PATCH 246/431] use https:// in ICU homepage --- easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb index c0e823ba2a7..17b26cee098 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-66.1-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'ICU' version = '66.1' -homepage = 'http://icu-project.org/' +homepage = 'https://icu-project.org/' description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.""" From 00204e50e703b68ed8833a52e8a3868b56cbbf36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 10:53:46 +0200 Subject: [PATCH 247/431] adding easyconfigs: Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb --- ...onito-0.1.4-fosscuda-2019b-Python-3.7.4.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..45b19c27d2e --- /dev/null +++ b/easybuild/easyconfigs/b/Bonito/Bonito-0.1.4-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,107 @@ +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('PyTorch', '1.3.1', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('Mako', '1.1.0'), + ('PyYAML', '5.1.2'), + ('apex', '20200325', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('toml', '0.10.0', { + 'checksums': ['229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c'], + }), + ('tqdm', '4.45.0', { + 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('alembic', '1.4.2', { + 'checksums': ['035ab00497217628bf5d0be82d664d8713ab13d37b630084da8e1f98facf4dbf'], + }), + ('cmd2', '1.0.1', { + 'checksums': ['d339166d8f65d342f37df01b7fb4820f9618209937d12e8f1af6245f12605c3a'], + }), + ('prettytable', '0.7.2', { + 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], + }), + ('cliff', '3.1.0', { + # drop too strict version requirements for cmd2 + 'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ", + 'checksums': ['529b0ee0d2d38c7cbbababbbe3472b43b667a5c36025ef1b6cd00851c4313849'], + }), + ('colorlog', '4.1.0', { + 'checksums': ['30aaef5ab2a1873dec5da38fd6ba568fa761c9fa10b40241027fa3edea47f3d2'], + }), + ('SQLAlchemy', '1.3.16', { + 'checksums': ['7224e126c00b8178dfd227bc337ba5e754b197a3867d33b9f30dc0208f773d70'], + }), + ('cmaes', '0.5.0', { + 'checksums': ['213d91a41f1d75b8cebca56477b8460da0fc757f9bbd1e5767023ad12711dfb4'], + }), + ('optuna', '1.3.0', { + 'checksums': ['a9fef67314833b694a9779ff63e9f0531d44a780a1ea0d8a9a097f2e8a33ab70'], + }), + ('parasail', '1.2', { + 'checksums': ['6ceef978e7d06293c38c9824f76557f3d7e137cb05487be31bf89286f7a8201e'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('pyperclip', '1.8.0', { + 'checksums': ['b75b975160428d84608c26edba2dec146e7799566aea42c1fe1b32e72b6028f2'], + }), + ('stevedore', '1.32.0', { + 'checksums': ['18afaf1d623af5950cc0f7e75e70f917784c73b652a34a12d90b309451b5500b'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.1.1', { + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), + ('fast-ctc-decode', '0.2.5', { + 'source_tmpl': 'fast_ctc_decode-%(version)s-cp37-cp37m-manylinux1_x86_64.whl', + 'unpack_sources': False, + 'checksums': ['b47976b2f951dade427a2f9ddc0ae6905561a76411941cf02b7f6e3e037f4062'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'checksums': ['3fc8df5ca099607eaabd745afd2de156d981b24f22e8b54ccaf53661b3dbb274'], + # strip out pinned versions for dependencies + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' From 4b058bbf595347c97ce7d04967cb36736d7daa38 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 28 Apr 2020 11:45:53 +0200 Subject: [PATCH 248/431] adding easyconfigs: pIRS-2.0.2-gompi-2019b.eb, Coreutils-8.32-GCCcore-8.3.0.eb and patches: pIRS-2.0.2_fix-Makefiles.patch --- .../Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb | 24 ++++ .../p/pIRS/pIRS-2.0.2-gompi-2019b.eb | 68 +++++++++ .../p/pIRS/pIRS-2.0.2_fix-Makefiles.patch | 130 ++++++++++++++++++ 3 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb create mode 100644 easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..91e06616f29 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "8.32" + +homepage = 'http://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the + GNU operating system. These are the core utilities which are expected to exist on every operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [('binutils', '2.32')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb new file mode 100644 index 00000000000..26d040ded04 --- /dev/null +++ b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb @@ -0,0 +1,68 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'pIRS' +version = '2.0.2' + +homepage = 'https://github.com/galaxy001/pirs' +description = """pIRS (profile based Illumina pair-end Reads Simulator) is a program for simulating paired-end reads +from a reference genome. It is optimized for simulating reads similar to those generated from the Illumina platform.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +# https://github.com/galaxy001/pirs +github_account = 'galaxy001' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-Makefiles.patch'] +checksums = [ + 'f80051819ee2c4307ad7ff74d35785c6ba864e8219673e6b0f12ff326eedb2e4', # v2.0.2.tar.gz + '5168b02abc5162b8c4175d76ee50f1bf876911b31449d21008c3c3464935d47f', # pIRS-2.0.2_fix-Makefiles.patch +] + +dependencies = [ + ('Perl', '5.30.0'), + ('zlib', '1.2.11'), + ('Boost', '1.71.0'), + ('gzip', '1.10'), + ('gnuplot', '5.2.8'), + ('SAMtools', '0.1.20'), + ('Coreutils', '8.32'), +] + +skipsteps = ['configure', 'install'] + +unpack_options = '--strip-components=1' +buildininstalldir = True + +buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" PKGDATADIR="%(installdir)s"' + +modextrapaths = {'PATH': ''} + +local_bins = ['gc_coverage_bias', 'pirs'] +local_perl_files = [ + 'alignment_stator', 'baseCalling_Matrix_analyzer', 'baseCalling_Matrix_calculator', + 'baseCalling_Matrix_merger', 'gc_coverage_bias_plot', 'indelstat_sam_bam' +] +sanity_check_paths = { + 'files': ['%s' % f for f in local_bins + local_perl_files], + 'dirs': [] +} + +sanity_check_commands = [ + # Binaries + ("gc_coverage_bias -h 2>&1 | grep 'it is a program to stat about the gc_depth'", ''), + ("pirs -h | grep 'pirs (Profile-based Illumina pair-end Reads Simulator)'", ''), + # Perl files + 'alignment_stator --help', + ("baseCalling_Matrix_analyzer -h 2>&1 | grep 'analyse the matrix about reads'", ''), + 'baseCalling_Matrix_calculator --help', + ("baseCalling_Matrix_merger -h 2>&1 | grep 'merge the baseCalling matrix together'", ''), + ("gc_coverage_bias_plot 2>&1 | grep 'gc_coverage_bias_plot '", ''), + ("indelstat_sam_bam --help 2>&1 | grep 'indelstat_sam_bam '", ''), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch new file mode 100644 index 00000000000..4f85f9bea34 --- /dev/null +++ b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch @@ -0,0 +1,130 @@ +Fix hardcoded stuff in Makefiles + +author: Pavel Grochal (INUITS) +diff -ru --new-file pirs-2.0.2.orig/Makefile pirs-2.0.2/Makefile +--- pirs-2.0.2.orig/Makefile 2016-08-14 07:10:03.000000000 +0200 ++++ pirs-2.0.2/Makefile 2020-04-28 10:34:20.369344282 +0200 +@@ -1,3 +1,10 @@ ++CC ?= gcc ++CXX ?= g++ ++CFLAGS ?= -g -O2 ++CXXFLAGS ?= -g -O2 ++PKGDATADIR ?= "/usr/local/share/pirs" ++export ++ + all: simulator stator symlinks + + PERL_LIST = stator/baseCallingMatrix/baseCalling_Matrix_analyzer \ +@@ -49,4 +56,3 @@ + git push github master + git push + git push google master +- +diff -ru --new-file pirs-2.0.2.orig/src/pirs/gccMakefile pirs-2.0.2/src/pirs/gccMakefile +--- pirs-2.0.2.orig/src/pirs/gccMakefile 2016-08-14 07:10:03.000000000 +0200 ++++ pirs-2.0.2/src/pirs/gccMakefile 2020-04-28 11:43:36.611256253 +0200 +@@ -1,52 +1,23 @@ +-CFLAGS = -pipe -mtune=generic -msse2 -fopenmp -DSFMT_MEXP=19937 -DHAVE_CONFIG_H -DPKGDATADIR='"/usr/local/share/pirs"' -I. -I.. -ISFMT-src-1.4 +- +-ifeq ($(shell uname -s),Darwin) +-CFLAGS += -march=core2 -Bstatic -L/opt/local/lib -I/opt/local/include +-else +-CFLAGS += -static +-endif +- +-#GCC_VERSION := `gcc -dumpversion` +-GCC_VERSION := $(shell gcc -dumpversion) +-GCC_MAJOR := $(shell echo $(GCC_VERSION) | cut -d'.' -f1) +-#GCC_MINOR := $(shell echo $(GCC_VERSION) | cut -d'.' -f2) +-#GCC_SUB := $(shell echo $(GCC_VERSION) | cut -d'.' -f3) +-GCC4_VER := $(shell echo $(GCC_VERSION) | cut -d'.' -f2,3) +- +-CPPFLAGS += $(CFLAGS) +- +-ifeq ($(GCC_MAJOR),4) +-ifeq ($(shell expr 2.4 \<= $(GCC4_VER)),1) +-CFLAGS += -march=native +-CPPFLAGS += -march=native +-endif +-ifeq ($(shell expr 3.6 \<= $(GCC4_VER)),1) +-#CPPFLAGS += -std=c++0x +-endif +-endif +- +-LDLIB = -lz -lpthread +-LDFLAGS = -Wl,-O1 -Wl,--sort-common -Wl,--enable-new-dtags -Wl,--hash-style=both $(LDLIB) + + SRCDIRS = . SFMT-src-1.4 + SRCEXTS = .C .cc .cpp .CPP .c++ .cxx .c +-OLevel= -O2 ++ + WARNFLAGS = -Wfloat-equal -Wall + SOURCES = $(foreach d,$(SRCDIRS),$(wildcard $(addprefix $(d)/*,$(SRCEXTS)))) + +-# g++ -DHAVE_CONFIG_H -I. -DSFMT_MEXP=19937 -DPKGDATADIR='"/usr/local/share/pirs"' -Wall -Wextra -msse2 -fopenmp -g -O2 *.cpp SFMT-src-1.4/SFMT.c -lz ++EXTRAFLAGS = -lz -lpthread -pipe -mtune=generic -msse2 -fopenmp -DSFMT_MEXP=19937 -DHAVE_CONFIG_H -I. -I.. -ISFMT-src-1.4 + + all: pirs + @echo Souce Files:[$(SOURCES)] + + pirs: $(SOURCES) +- g++ $(WARNFLAGS) $(CPPFLAGS) $(OLevel) -o $@ $^ $(LDFLAGS) ++ $(CXX) $(WARNFLAGS) $(CPPFLAGS) -o $@ $^ $(LDFLAGS) $(EXTRAFLAGS) -DPKGDATADIR='"$(PKGDATADIR)"' + + dpirs: $(SOURCES) +- g++ $(WARNFLAGS) $(CPPFLAGS) $(OLevel) -g -DWITH_DEBUG -o $@ $^ $(LDFLAGS) ++ $(CXX) $(WARNFLAGS) $(CPPFLAGS) -g -DWITH_DEBUG -o $@ $^ $(LDFLAGS) $(EXTRAFLAGS) -DPKGDATADIR='"$(PKGDATADIR)"' + + hmap: +- g++ -M -MM *.cpp ++ $(CXX) $(CPPFLAGS) -M -MM *.cpp + + test: pirs + cd test && sh pirs.sh +diff -ru --new-file pirs-2.0.2.orig/src/stator/gcContCvgBias/Makefile pirs-2.0.2/src/stator/gcContCvgBias/Makefile +--- pirs-2.0.2.orig/src/stator/gcContCvgBias/Makefile 2016-08-14 07:10:03.000000000 +0200 ++++ pirs-2.0.2/src/stator/gcContCvgBias/Makefile 2020-04-28 11:39:44.227050586 +0200 +@@ -1,38 +1,16 @@ +-ifeq ($(shell uname -s),Darwin) +-CPPFLAGS += -march=core2 -Bstatic -L/opt/local/lib -I/opt/local/include +-else +-CPPFLAGS += -static +-endif +- +-GCC_VERSION := $(shell gcc -dumpversion) +-GCC_MAJOR := $(shell echo $(GCC_VERSION) | cut -d'.' -f1) +-GCC4_VER := $(shell echo $(GCC_VERSION) | cut -d'.' -f2,3) +- +-ifeq ($(GCC_MAJOR),4) +-ifeq ($(shell expr 2.4 \<= $(GCC4_VER)),1) +-CPPFLAGS += -march=native +-endif +-ifeq ($(shell expr 3.6 \<= $(GCC4_VER)),1) +-CPPFLAGS += -std=c++0x +-endif +-endif +- + + OBJ = gzstream.o self_util.o main.o stat_soap_coverage.o +-CC = g++ +-LIBRARY = -O3 -pipe $(CPPFLAGS) -mtune=generic -pedantic -Wfloat-equal \ +-#-Wall + + gc_coverage_bias:${OBJ} +- ${CC} -o gc_coverage_bias ${LIBRARY} ${OBJ} -lz ++ ${CXX} $(CPPFLAGS) -o gc_coverage_bias $(LDFLAGS) ${OBJ} -lz + gzstream.o:gzstream.h gzstream.cpp +- ${CC} -c ${LIBRARY} gzstream.h gzstream.cpp ++ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) gzstream.h gzstream.cpp + self_util.o:self_util.cpp self_util.h +- ${CC} -c ${LIBRARY} self_util.cpp self_util.h ++ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) self_util.cpp self_util.h + main.o:main.cpp +- ${CC} -c ${LIBRARY} main.cpp ++ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) main.cpp + stat_soap_coverage.o:stat_soap_coverage.h stat_soap_coverage.cpp +- ${CC} -c ${LIBRARY} stat_soap_coverage.h stat_soap_coverage.cpp ++ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) stat_soap_coverage.h stat_soap_coverage.cpp + + test: gc_coverage_bias + ./gc_coverage_bias -r gcdeptestref.fa.gz -o test -w 100,200 --gcdump --depwindump gcdeptest.depth.gz From 25da613a77d42146cf30d44ef59cdf24109a5bb2 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 28 Apr 2020 13:55:57 +0200 Subject: [PATCH 249/431] fixed remarks --- .../Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb | 1 + .../p/pIRS/pIRS-2.0.2-gompi-2019b.eb | 33 ++++++++++++------- .../p/pIRS/pIRS-2.0.2_fix-Makefiles.patch | 22 ++++++------- 3 files changed, 34 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb index 91e06616f29..0c44c947197 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb @@ -13,6 +13,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['4458d8de7849df44ccab15e16b1548b285224dbba5f08fac070c1c0e0bcc4cfa'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb index 26d040ded04..1780cbb9d7f 100644 --- a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb @@ -1,7 +1,7 @@ # Author: Pavel Grochal (INUITS) # License: GPLv2 -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'pIRS' version = '2.0.2' @@ -11,7 +11,7 @@ description = """pIRS (profile based Illumina pair-end Reads Simulator) is a pro from a reference genome. It is optimized for simulating reads similar to those generated from the Illumina platform.""" toolchain = {'name': 'gompi', 'version': '2019b'} -toolchainopts = {'cstd': 'c++11'} +toolchainopts = {'cstd': 'c++11', 'openmp': True} # https://github.com/galaxy001/pirs github_account = 'galaxy001' @@ -20,7 +20,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_fix-Makefiles.patch'] checksums = [ 'f80051819ee2c4307ad7ff74d35785c6ba864e8219673e6b0f12ff326eedb2e4', # v2.0.2.tar.gz - '5168b02abc5162b8c4175d76ee50f1bf876911b31449d21008c3c3464935d47f', # pIRS-2.0.2_fix-Makefiles.patch + '61cd267caeffd28eb7e53fb676d9c204ba1608cd4101f49fd17201bd3338d016', # pIRS-2.0.2_fix-Makefiles.patch ] dependencies = [ @@ -33,25 +33,36 @@ dependencies = [ ('Coreutils', '8.32'), ] -skipsteps = ['configure', 'install'] - -unpack_options = '--strip-components=1' -buildininstalldir = True - buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" PKGDATADIR="%(installdir)s"' -modextrapaths = {'PATH': ''} - local_bins = ['gc_coverage_bias', 'pirs'] local_perl_files = [ 'alignment_stator', 'baseCalling_Matrix_analyzer', 'baseCalling_Matrix_calculator', 'baseCalling_Matrix_merger', 'gc_coverage_bias_plot', 'indelstat_sam_bam' ] + +files_to_copy = [ + (['src/stator/alignment_stator.pl', + 'src/stator/baseCallingMatrix/baseCalling_Matrix_analyzer.pl', + 'src/stator/baseCallingMatrix/baseCalling_Matrix_calculator.pl', + 'src/stator/baseCallingMatrix/baseCalling_Matrix_merger.pl', + 'src/stator/gcContCvgBias/gc_coverage_bias', + 'src/stator/gcContCvgBias/gc_coverage_bias_plot.pl', + 'src/stator/indelstat_sam_bam.pl', + 'src/pirs/pirs', + 'src/pirs/Profiles', + ], 'bin'), +] + +# cd to bin dir and make link for all perl files +postinstallcmds = [" && ". join(['cd %(installdir)s/bin'] + ["ln -s %s.pl %s" % (f, f) for f in local_perl_files])] + sanity_check_paths = { - 'files': ['%s' % f for f in local_bins + local_perl_files], + 'files': ['bin/%s' % f for f in local_bins + local_perl_files], 'dirs': [] } +# grep is used here because most of the 'help' commands below returns non-zero exit codes sanity_check_commands = [ # Binaries ("gc_coverage_bias -h 2>&1 | grep 'it is a program to stat about the gc_depth'", ''), diff --git a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch index 4f85f9bea34..9bae3be99fb 100644 --- a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch +++ b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2_fix-Makefiles.patch @@ -22,7 +22,7 @@ diff -ru --new-file pirs-2.0.2.orig/Makefile pirs-2.0.2/Makefile - diff -ru --new-file pirs-2.0.2.orig/src/pirs/gccMakefile pirs-2.0.2/src/pirs/gccMakefile --- pirs-2.0.2.orig/src/pirs/gccMakefile 2016-08-14 07:10:03.000000000 +0200 -+++ pirs-2.0.2/src/pirs/gccMakefile 2020-04-28 11:43:36.611256253 +0200 ++++ pirs-2.0.2/src/pirs/gccMakefile 2020-04-28 13:31:25.328907461 +0200 @@ -1,52 +1,23 @@ -CFLAGS = -pipe -mtune=generic -msse2 -fopenmp -DSFMT_MEXP=19937 -DHAVE_CONFIG_H -DPKGDATADIR='"/usr/local/share/pirs"' -I. -I.. -ISFMT-src-1.4 - @@ -62,28 +62,28 @@ diff -ru --new-file pirs-2.0.2.orig/src/pirs/gccMakefile pirs-2.0.2/src/pirs/gcc SOURCES = $(foreach d,$(SRCDIRS),$(wildcard $(addprefix $(d)/*,$(SRCEXTS)))) -# g++ -DHAVE_CONFIG_H -I. -DSFMT_MEXP=19937 -DPKGDATADIR='"/usr/local/share/pirs"' -Wall -Wextra -msse2 -fopenmp -g -O2 *.cpp SFMT-src-1.4/SFMT.c -lz -+EXTRAFLAGS = -lz -lpthread -pipe -mtune=generic -msse2 -fopenmp -DSFMT_MEXP=19937 -DHAVE_CONFIG_H -I. -I.. -ISFMT-src-1.4 ++EXTRAFLAGS = -lz -lpthread -pipe -DSFMT_MEXP=19937 -DHAVE_CONFIG_H -I. -I.. -ISFMT-src-1.4 -DPKGDATADIR='"$(PKGDATADIR)"' all: pirs @echo Souce Files:[$(SOURCES)] pirs: $(SOURCES) - g++ $(WARNFLAGS) $(CPPFLAGS) $(OLevel) -o $@ $^ $(LDFLAGS) -+ $(CXX) $(WARNFLAGS) $(CPPFLAGS) -o $@ $^ $(LDFLAGS) $(EXTRAFLAGS) -DPKGDATADIR='"$(PKGDATADIR)"' ++ $(CXX) $(WARNFLAGS) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) $(EXTRAFLAGS) dpirs: $(SOURCES) - g++ $(WARNFLAGS) $(CPPFLAGS) $(OLevel) -g -DWITH_DEBUG -o $@ $^ $(LDFLAGS) -+ $(CXX) $(WARNFLAGS) $(CPPFLAGS) -g -DWITH_DEBUG -o $@ $^ $(LDFLAGS) $(EXTRAFLAGS) -DPKGDATADIR='"$(PKGDATADIR)"' ++ $(CXX) $(WARNFLAGS) $(CXXFLAGS) -g -DWITH_DEBUG -o $@ $^ $(LDFLAGS) $(EXTRAFLAGS) hmap: - g++ -M -MM *.cpp -+ $(CXX) $(CPPFLAGS) -M -MM *.cpp ++ $(CXX) $(CXXFLAGS) -M -MM *.cpp test: pirs cd test && sh pirs.sh diff -ru --new-file pirs-2.0.2.orig/src/stator/gcContCvgBias/Makefile pirs-2.0.2/src/stator/gcContCvgBias/Makefile --- pirs-2.0.2.orig/src/stator/gcContCvgBias/Makefile 2016-08-14 07:10:03.000000000 +0200 -+++ pirs-2.0.2/src/stator/gcContCvgBias/Makefile 2020-04-28 11:39:44.227050586 +0200 ++++ pirs-2.0.2/src/stator/gcContCvgBias/Makefile 2020-04-28 13:35:00.329179368 +0200 @@ -1,38 +1,16 @@ -ifeq ($(shell uname -s),Darwin) -CPPFLAGS += -march=core2 -Bstatic -L/opt/local/lib -I/opt/local/include @@ -112,19 +112,19 @@ diff -ru --new-file pirs-2.0.2.orig/src/stator/gcContCvgBias/Makefile pirs-2.0.2 gc_coverage_bias:${OBJ} - ${CC} -o gc_coverage_bias ${LIBRARY} ${OBJ} -lz -+ ${CXX} $(CPPFLAGS) -o gc_coverage_bias $(LDFLAGS) ${OBJ} -lz ++ ${CXX} $(CXXFLAGS) -o gc_coverage_bias $(LDFLAGS) ${OBJ} -lz gzstream.o:gzstream.h gzstream.cpp - ${CC} -c ${LIBRARY} gzstream.h gzstream.cpp -+ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) gzstream.h gzstream.cpp ++ ${CXX} $(CXXFLAGS) -c $(LDFLAGS) gzstream.h gzstream.cpp self_util.o:self_util.cpp self_util.h - ${CC} -c ${LIBRARY} self_util.cpp self_util.h -+ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) self_util.cpp self_util.h ++ ${CXX} $(CXXFLAGS) -c $(LDFLAGS) self_util.cpp self_util.h main.o:main.cpp - ${CC} -c ${LIBRARY} main.cpp -+ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) main.cpp ++ ${CXX} $(CXXFLAGS) -c $(LDFLAGS) main.cpp stat_soap_coverage.o:stat_soap_coverage.h stat_soap_coverage.cpp - ${CC} -c ${LIBRARY} stat_soap_coverage.h stat_soap_coverage.cpp -+ ${CXX} $(CPPFLAGS) -c $(LDFLAGS) stat_soap_coverage.h stat_soap_coverage.cpp ++ ${CXX} $(CXXFLAGS) -c $(LDFLAGS) stat_soap_coverage.h stat_soap_coverage.cpp test: gc_coverage_bias ./gc_coverage_bias -r gcdeptestref.fa.gz -o test -w 100,200 --gcdump --depwindump gcdeptest.depth.gz From a3387ff75b659889b2ec1211513f90695f0f52f9 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 28 Apr 2020 14:01:34 +0200 Subject: [PATCH 250/431] added 'make test' and bumped samtools version --- easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb index 1780cbb9d7f..05615326392 100644 --- a/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/pIRS/pIRS-2.0.2-gompi-2019b.eb @@ -29,12 +29,14 @@ dependencies = [ ('Boost', '1.71.0'), ('gzip', '1.10'), ('gnuplot', '5.2.8'), - ('SAMtools', '0.1.20'), + ('SAMtools', '1.10'), ('Coreutils', '8.32'), ] buildopts = 'CC="$CC" CXX="$CXX" CFLAGS="$CFLAGS" CXXFLAGS="$CXXFLAGS" PKGDATADIR="%(installdir)s"' +runtest = 'test' + local_bins = ['gc_coverage_bias', 'pirs'] local_perl_files = [ 'alignment_stator', 'baseCalling_Matrix_analyzer', 'baseCalling_Matrix_calculator', From 586cc61a63e05240309b3e4c015219becf574883 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 28 Apr 2020 14:22:14 +0200 Subject: [PATCH 251/431] fixed https --- .../easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb index 0c44c947197..0acb224e69e 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-8.32-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = "Coreutils" version = "8.32" -homepage = 'http://www.gnu.org/software/coreutils/' +homepage = 'https://www.gnu.org/software/coreutils/' description = """The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. """ From f9f2ad6c4bd7c8021c2d9374ebe5730cc4b7310e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Apr 2020 16:42:32 +0200 Subject: [PATCH 252/431] adding easyconfigs: glew-2.1.0-GCCcore-8.3.0.eb --- .../g/glew/glew-2.1.0-GCCcore-8.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..9b3901c4314 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb @@ -0,0 +1,42 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library + +The OpenGL Extension Wrangler Library (GLEW) is a cross-platform +open-source C/C++ extension loading library. GLEW provides +efficient run-time mechanisms for determining which OpenGL +extensions are supported on the target platform. OpenGL +core and extension functionality is exposed in a single header +file. GLEW has been tested on a variety of operating systems, +including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('Mesa', '19.2.1')] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/glew.h', 'include/GL/glxew.h', 'include/GL/wglew.h'], + 'dirs': ['', ] +} + +moduleclass = 'devel' From 8507e945af03655b1e0d7f383b18f4975498243f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Apr 2020 16:43:38 +0200 Subject: [PATCH 253/431] adding easyconfigs: ctffind-4.1.13-fosscuda-2019b.eb --- .../ctffind/ctffind-4.1.13-fosscuda-2019b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019b.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019b.eb new file mode 100644 index 00000000000..e50df030895 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.13' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] +checksums = [ + '48231f8511b222176ea39b80c58ae8fb8a6bac5e0da247c54f5a84b52c8750cf', # ctffind-4.1.13.tar.gz + # ctffind-4.1.13_remove_bogus_include_lines.patch + 'ae218a61a24cec2e35fa4a7ddd497c0d1bb997957bfeb8866d941442afe26365', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.3'), + ('LibTIFF', '4.0.10'), + ('GSL', '2.6'), + ('wxWidgets', '3.1.3'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From d0d1fcb11341ad5fc6cfa9484e2fac60612e2695 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 28 Apr 2020 17:27:42 +0200 Subject: [PATCH 254/431] adding easyconfigs: MotionCor2-1.3.1-GCCcore-8.3.0.eb --- .../MotionCor2-1.3.1-GCCcore-8.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..dfaa5e0b7fd --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.3.1' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +sources = [ + '%(name)s_%(version)s.zip', +] +checksums = [ + 'b8b7c6f7751af4a60c15dc1159ddd20afc87d1400cb29982728f463753153558', # MotionCor2_1.3.1.zip +] + +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.32'), + ('CUDA', '10.1.243', '', True), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.3'), + ('XZ', '5.2.4'), + ('LibTIFF', '4.0.10'), + ('jbigkit', '2.1'), +] + +moduleclass = 'bio' From 05dabd18524529866222d00a651d13138108a480 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Apr 2020 17:37:24 +0200 Subject: [PATCH 255/431] Downgrade Mesa --- easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb index 9b3901c4314..8558cea5270 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] builddependencies = [('binutils', '2.32')] -dependencies = [('Mesa', '19.2.1')] +dependencies = [('Mesa', '19.1.7')] skipsteps = ['configure'] From 33e3a3b3818ecda7ab46f634ed9ff7a754198555 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 18:14:45 +0200 Subject: [PATCH 256/431] adding easyconfigs: FLASH-1.2.11-GCC-8.3.0.eb --- .../f/FLASH/FLASH-1.2.11-GCC-8.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-GCC-8.3.0.eb b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-GCC-8.3.0.eb new file mode 100644 index 00000000000..cc46f9d2ca6 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-1.2.11-GCC-8.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '1.2.11' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software + tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to + merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. + The resulting longer reads can significantly improve genome assemblies. They can also improve + transcriptome assembly when FLASH is used to merge RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['http://download.sourceforge.net/%(namelower)spage'] +sources = [SOURCE_TAR_GZ] +checksums = ['685ca6f7fedda07434d8ee03c536f4763385671c4509c5bb48beb3055fd236ac'] + +dependencies = [('zlib', '1.2.11')] + +files_to_copy = [(['flash'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash'], + 'dirs': [], +} + +moduleclass = 'bio' From b8080a411d93d911294a5397eaa7c9fb15e2c707 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Tue, 28 Apr 2020 18:52:26 +0200 Subject: [PATCH 257/431] adding easyconfigs: torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb, torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb --- ...orchaudio-0.5.0-foss-2019b-Python-3.7.4.eb | 28 +++++++++++++++++++ ...audio-0.5.0-fosscuda-2019b-Python-3.7.4.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..044fc75d85a --- /dev/null +++ b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'torchaudio' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/audio' +description = """ Data manipulation and transformation for audio signal +processing, powered by PyTorch """ + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/audio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca27317dddcbe69c6586b03885534b3b50d666580843a5d22f1d605d47551807'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('PyTorch', '1.4.0', versionsuffix), + ('SoX', '14.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..d003fc3a66f --- /dev/null +++ b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'torchaudio' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/audio' +description = """ Data manipulation and transformation for audio signal +processing, powered by PyTorch """ + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/audio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca27317dddcbe69c6586b03885534b3b50d666580843a5d22f1d605d47551807'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('PyTorch', '1.4.0', versionsuffix), + ('SoX', '14.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From f16a5cff54a0c985a5d3ff9465cd7857da2f8647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 19:53:01 +0200 Subject: [PATCH 258/431] adding easyconfigs: MultiQC-1.8-intel-2019b-Python-3.7.4.eb --- .../MultiQC-1.8-intel-2019b-Python-3.7.4.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..06577a12e1d --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,73 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('matplotlib', '3.1.1', versionsuffix), + ('PyYAML', '5.1.2'), + ('networkx', '2.4', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('simplejson', '3.17.0', { + 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], + }), + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('humanfriendly', '8.2', { + 'checksums': ['bf52ec91244819c780341a3438d5d7b09f431d3f113a475147ac9b7b167a3d12'], + }), + ('coloredlogs', '14.0', { + 'checksums': ['a1fab193d2053aa6c0a97608c4342d031f1f93a3d1218432c59322441d31a505'], + }), + ('multiqc', version, { + 'checksums': ['ea7f3e320a8812a0d5a8778605f76ff4bb6ca5c3ed23d4269f0bac2159838f3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 3265ebd98f67e6d96b8cd25cf7e53413b5b65d3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 20:03:05 +0200 Subject: [PATCH 259/431] {lang}[foss/2020a] R v4.0.0 (WIP, extensions should be updated) --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 2332 +++++++++++++++++ 1 file changed, 2332 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb new file mode 100644 index 00000000000..81ff1b42e7d --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -0,0 +1,2332 @@ +name = 'R' +version = '4.0.0' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', '20200222'), + ('Mesa', '20.0.2'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.31.1'), + ('PCRE', '8.44'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.4'), # for plottting in R + ('LibTIFF', '4.1.0'), + ('Java', '11', '', True), + ('Tk', '8.6.10'), # for tcltk + ('cURL', '7.69.1'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.0'), # for igraph + ('NLopt', '2.6.1'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '66.1'), # for rJava & gdsfmt + ('HDF5', '1.10.6'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.10-1'), # for animation + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1e'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 25 March 2020 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'checksums': ['b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.4', { + 'checksums': ['d992fe8f7480606a0790be94948a6b667f37aa607ccd5e5613e88af861bb00d5'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '1.1-15.2', { + 'checksums': ['0b83e78385293d6cdc0189a07fcc3f9f9db286c8c4af3288467f5257e79cb28b'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '2.2-14', { + 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], + }), + ('bnlearn', '4.5', { + 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('formatR', '1.7', { + 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], + }), + ('gtools', '3.8.1', { + 'checksums': ['051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': 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['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.6.0', { + 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0', { + 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], + }), + ('topicmodels', '0.2-9', { + 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], + }), + ('tidytext', '0.2.3', { + 'checksums': ['c103f98f5cbbb5a4ea4c893520ea5eb38b9c5097e5325d7efd4f7e3afe71068b'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-1', { + 'checksums': ['520ef83e9a7c58e3c5b7175fbda902b747b2e01c24b53714ede81a6a87de5b64'], + }), + ('loo', '2.2.0', { + 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'], + }), + ('StanHeaders', '2.21.0-1', { + 'checksums': ['4e94148af2960f203b208c2b725d8be628ca282c7a1e967a7e6e78aa5eb90d3f'], + }), + ('rstan', '2.19.3', { + 'checksums': ['d7025dccdc2337fd0cf3b9689c3e0a07558a47a08b7cbc370e0b3998256f1689'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), +] + +moduleclass = 'lang' From 84dcf440562306f0d7ac6f45a2fac25e6276b7dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 20:09:22 +0200 Subject: [PATCH 260/431] adding easyconfigs: MultiQC-1.8-intel-2019b-Python-2.7.16.eb --- .../MultiQC-1.8-intel-2019b-Python-2.7.16.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..7851c93c45d --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb @@ -0,0 +1,79 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '2.7.16'), + ('matplotlib', '2.2.4', versionsuffix), + ('PyYAML', '5.1.2'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('networkx', '2.2', { + 'source_tmpl': 'networkx-%(version)s.zip', + 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], + }), + ('simplejson', '3.17.0', { + 'checksums': ['2b4b2b738b3b99819a17feaf118265d0753d5536049ea570b3c43b51c4701e81'], + }), + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.1.1', { + 'checksums': ['2e50876bcdd74517e7b71f3e7a76102050edec255b3983403f1a63e7c8a41e7a'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('monotonic', '1.5', { + 'checksums': ['23953d55076df038541e648a53676fb24980f7a1be290cdda21300b3bc21dfb0'], + }), + ('humanfriendly', '8.2', { + 'checksums': ['bf52ec91244819c780341a3438d5d7b09f431d3f113a475147ac9b7b167a3d12'], + }), + ('coloredlogs', '14.0', { + 'checksums': ['a1fab193d2053aa6c0a97608c4342d031f1f93a3d1218432c59322441d31a505'], + }), + ('multiqc', version, { + 'checksums': ['ea7f3e320a8812a0d5a8778605f76ff4bb6ca5c3ed23d4269f0bac2159838f3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 76810dc05f1997da2bba64d80075203075dc586c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Apr 2020 20:41:58 +0200 Subject: [PATCH 261/431] copy easyconfigs using GCCcore/9.3.0 toolchain from 2020a branch into develop --- .../a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb | 39 +++++++++++ ...chspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb | 34 +++++++++ .../at-spi2-atk-2.34.2-GCCcore-9.3.0.eb | 37 ++++++++++ .../at-spi2-core-2.36.0-GCCcore-9.3.0.eb | 39 +++++++++++ .../a/attr/attr-2.4.48-GCCcore-9.3.0.eb | 26 +++++++ .../easyconfigs/b/BWA/BWA-0.7.17-GCC-9.3.0.eb | 37 ++++++++++ .../b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb | 23 +++++++ .../b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb | 36 ++++++++++ .../c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb | 56 +++++++++++++++ .../d/DB/DB-18.1.32-GCCcore-9.3.0.eb | 29 ++++++++ .../d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb | 26 +++++++ .../f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb | 44 ++++++++++++ .../f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb | 34 +++++++++ .../GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb | 53 ++++++++++++++ .../GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb | 33 +++++++++ ...ction-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb | 44 ++++++++++++ .../g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb | 69 +++++++++++++++++++ .../Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb | 46 +++++++++++++ .../g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb | 36 ++++++++++ .../g/gc/gc-7.6.12-GCCcore-9.3.0.eb | 40 +++++++++++ .../g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb | 35 ++++++++++ .../g/glew/glew-2.1.0-GCCcore-9.3.0.eb | 36 ++++++++++ .../g/glog/glog-0.4.0-GCCcore-9.3.0.eb | 32 +++++++++ .../g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb | 56 +++++++++++++++ .../h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb | 37 ++++++++++ .../HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb | 35 ++++++++++ ...thesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb | 33 +++++++++ .../l/LAME/LAME-3.100-GCCcore-9.3.0.eb | 33 +++++++++ .../l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb | 34 +++++++++ .../l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb | 27 ++++++++ .../libarchive-3.4.2-GCCcore-9.3.0.eb | 29 ++++++++ .../l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb | 33 +++++++++ .../libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb | 36 ++++++++++ .../libffcall/libffcall-2.2-GCCcore-9.3.0.eb | 33 +++++++++ .../l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb | 35 ++++++++++ .../libgeotiff-1.5.1-GCCcore-9.3.0.eb | 36 ++++++++++ .../libmatheval-1.1.11-GCCcore-9.3.0.eb | 38 ++++++++++ .../libsigsegv-2.12-GCCcore-9.3.0.eb | 26 +++++++ .../libsodium-1.0.18-GCCcore-9.3.0.eb | 33 +++++++++ .../libunistring-0.9.10-GCCcore-9.3.0.eb | 33 +++++++++ .../l/libxc/libxc-4.3.4-GCC-9.3.0.eb | 49 +++++++++++++ .../l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb | 32 +++++++++ .../m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb | 38 ++++++++++ .../m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb | 38 ++++++++++ .../m/MPFR/MPFR-4.0.2_include_float.patch | 10 +++ .../mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb | 29 ++++++++ .../o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb | 31 +++++++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb | 36 ++++++++++ .../o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb | 25 +++++++ .../p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb | 47 +++++++++++++ .../p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb | 42 +++++++++++ .../p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb | 41 +++++++++++ ...Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 34 +++++++++ .../p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb | 27 ++++++++ ...config-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb | 34 +++++++++ .../r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb | 28 ++++++++ .../s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb | 35 ++++++++++ .../s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb | 35 ++++++++++ .../SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb | 44 ++++++++++++ .../s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb | 24 +++++++ .../s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb | 36 ++++++++++ .../s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb | 49 +++++++++++++ .../t/tbb/tbb-2020.1-GCCcore-9.3.0.eb | 18 +++++ .../v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb | 30 ++++++++ .../v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb | 37 ++++++++++ .../w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb | 41 +++++++++++ .../x/x264/x264-20191217-GCCcore-9.3.0.eb | 37 ++++++++++ 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easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.0.2_include_float.patch create mode 100644 easybuild/easyconfigs/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20191217-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..823b5ab392a --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), +] + +dependencies = [ + ('GLib', '2.64.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..2814e8cb2f3 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_SOURCE] +sources = ['archspec-%(version)s-py2.py3-none-any.whl'] +checksums = ['12f2029f63ffbc560e43f7d1f366a45ff46c7bd0751653227f8015f83f121119'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('Python', '3.8.2')] + +unpack_sources = False + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b546bc7eab9 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.2-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.34.2' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['901323cee0eef05c01ec4dee06c701aeeca81a314a7d60216fa363005e27f4f0'] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.64.1'), + ('DBus', '1.13.12'), + ('at-spi2-core', '2.36.0'), + ('libxml2', '2.9.10'), + ('ATK', '2.36.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..2b9805f939c --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.36.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['88da57de0a7e3c60bc341a974a80fdba091612db3547c410d6deab039ca5c05a'] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), + ('gettext', '0.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.64.1'), + ('DBus', '1.13.12'), + ('X11', '20200222'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/attr/attr-2.4.48-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.4.48-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d98f3d7c65c --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.4.48-GCCcore-9.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.4.48' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ead72b358ec709ed00bbf7a9eaef1654baad937c001c044fe8b74c57f5324e7'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-9.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-9.3.0.eb new file mode 100644 index 00000000000..30d800ef414 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-9.3.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman, Big Data Institute, University of Oxford +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +dependencies = [ + ('Perl', '5.30.2'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb new file mode 100644 index 00000000000..eb8f188f4b0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.2.3-GCC-9.3.0.eb @@ -0,0 +1,23 @@ +name = 'Bowtie' +version = '1.2.3' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = [ + {'download_filename': '%(namelower)s-src-x86_64.zip', + 'filename': '%(namelower)s-%(version)s-src.zip'} +] +checksums = ['44e99f4ea8f731c36c556b1ff4108f50f89ee6896f1ba89377feb7c460c3b16e'] + +dependencies = [ + ('tbb', '2020.1'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb new file mode 100644 index 00000000000..279170f1b0e --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.4.1' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22'] + +dependencies = [ + ('tbb', '2020.1'), + ('zlib', '1.2.11'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..92d5988caaf --- /dev/null +++ b/easybuild/easyconfigs/c/CLISP/CLISP-2.49-GCCcore-9.3.0.eb @@ -0,0 +1,56 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'CLISP' +version = '2.49' + +homepage = 'https://clisp.sourceforge.io/' + +description = """ + Common Lisp is a high-level, general-purpose, object-oriented, dynamic, + functional programming language. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE + '/release/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['CLISP-%(version)s_fix-readline.patch'] + +checksums = [ + '8132ff353afaa70e6b19367a25ae3d5a43627279c25647c220641fed00f8e890', # clisp-2.49.tar.bz2 + '903ca7367721e5bfe216fd8151659c4d127739311fac61f812e0031faec100ea', # CLISP-2.49_fix-readline.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('DB', '18.1.32'), + ('libffcall', '2.2'), + ('libreadline', '8.0'), + ('libsigsegv', '2.12'), + ('PCRE', '8.44'), + ('zlib', '1.2.11'), +] + +configopts = 'build' + +# disable "streams" test due to problems with https:// +# see https://sourceforge.net/p/clisp/mailman/message/36224219/ +prebuildopts = "sed -e 's/\"streams\"/\"streamslong\"/' -i.eb tests/tests.lisp && cd build && " +buildopts = 'all check' + +parallel = 1 + +preinstallopts = 'cd build && ' + +sanity_check_paths = { + 'files': ['bin/clisp', 'lib/%(namelower)s-%(version)s/base/lisp.a'], + 'dirs': ['share/aclocal', 'share/doc'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..39fc5d2137e --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +# EasyBuild easyconfig +name = 'DB' +version = '18.1.32' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +# download via +# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, +# requires registration +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..6eb61cc1dba --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb @@ -0,0 +1,26 @@ +name = 'Doxygen' +version = '1.8.17' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['2cba988af2d495541cbbe5541b3bee0ee11144dcb23a81eada19f5501fd8b599'] + +builddependencies = [ + ('binutils', '2.34'), + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), +] + + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..ebdcd7df2f4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.2.2-GCCcore-9.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.2.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b620d187c26f76ca19e74210a0336c3b8380b97730df5cdf45f3e69e89000e5c'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('NASM', '2.14.02'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('x264', '20191217'), + ('LAME', '3.100'), + ('x265', '3.3'), + ('X11', '20200222'), + ('freetype', '2.10.1'), + ('fontconfig', '2.13.92'), + ('FriBidi', '1.0.9'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cef1dc631bb --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.9' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c5e47ea9026fb60da1944da9888b4e0a18854a0e2410bbfe7ad90a054d36e0c7'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb new file mode 100644 index 00000000000..dfdc787c512 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.1.5.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +dependencies = [ + ('Java', '11', '', True), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..6bec3cd41c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-GCC-9.3.0-Python-3.8.2.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-3.7.2_fix-Python3.patch'] +checksums = [ + '4258af4308deb9dbb5047379026b4cd9838513627cb943a44e16c40e42ae17f7', # geos-3.8.1.tar.bz2 + 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch +] + +dependencies = [('Python', '3.8.2')] + +builddependencies = [('SWIG', '4.0.1')] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..b8944994451 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.64.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.64.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eac05a63091c81adfdc8ef34820bcc7e7778c5b9e34734d344fc9e69ddf4fc82'] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('cairo', '1.16.0'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('GLib', '2.64.1'), + ('libffi', '3.3'), + ('util-linux', '2.35'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0fac0e6076c --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb @@ -0,0 +1,69 @@ +easyblock = 'Bundle' + +name = 'GTK+' +version = '3.24.17' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [ + ('binutils', '2.34'), + ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), + ('gettext', '0.20.1'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.30.2'), +] + +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.34.2'), + ('Gdk-Pixbuf', '2.40.0'), + ('Pango', '1.44.7'), + ('libepoxy', '1.5.4'), + ('X11', '20200222'), + ('FriBidi', '1.0.9'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.36.0', { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['1a172112b6da482d3be3de6a0c1c1762886e61e12b4315ae1aae9b69da1ed518'], + }), + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['f210255b221cb0f0db3e7b21399983b715c9dda6eb1e5c2f7fdf38f4f1b6bac0'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..ace94394831 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.40.0' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = [ + '1582595099537ca8ff3b99c6804350b4c058bb8ad67411bbaae024ee7cead4e6', # gdk-pixbuf-2.40.0.tar.xz +] + +builddependencies = [ + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), +] + +dependencies = [ + ('GLib', '2.64.1'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('X11', '20200222'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dgir=true " + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..473db350c1f --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'https://www.gnu.org/software/guile/' +description = """Guile is a programming language, designed to help programmers create flexible applications that + can be extended by users or other programmers with plug-ins, modules, or scripts.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3471fed2e72e5b04ad133bbaaf16369e8360283679bcf19800bc1b381024050'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.34'), +] +dependencies = [ + ('libunistring', '0.9.10'), + ('libffi', '3.3'), + ('gc', '7.6.12'), + ('GMP', '6.2.0'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ['bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', + 'include/libguile.h', 'lib/libguile.a', 'lib/libguile.%s' % SHLIB_EXT, + 'lib/pkgconfig/guile-%(version_major_minor)s.pc'], + 'dirs': ['include/guile'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0f5e45cde25 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.6.12-GCCcore-9.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.6.12' + +homepage = 'https://hboehm.info/gc/' + +description = """ + The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'https://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/releases/download/v%(version)s/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-7.6.10.tar.gz', +] +checksums = [ + '6cafac0d9365c2f8604f930aabd471145ac46ab6f771e835e57995964e845082', # gc-7.6.12.tar.gz + '587edf60817f56daf1e1ab38a4b3c729b8e846ff67b4f62a6157183708f099af', # libatomic_ops-7.6.10.tar.gz +] + +builddependencies = [ + ('binutils', '2.34'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..9433d212418 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a0965a5fb11 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('Mesa', '20.0.2')] + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all' + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': ['', ] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cab2d201006 --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'glog' +version = '0.4.0' + +homepage = 'https://github.com/google/glog' +description = "A C++ implementation of the Google logging module." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/google/glog/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f28359aeba12f30d73d9e4711ef356dc842886968112162bc73002645139c39c'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +dependencies = [ + ('gflags', '2.2.2'), + ('libunwind', '1.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..3d1fd89d8b7 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.8-GCCcore-9.3.0.eb @@ -0,0 +1,56 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.2.8' + +homepage = 'https://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['60a6764ccf404a1668c140f11cc1f699290ab70daa1151bb58fed6139a28ac37'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), + ('Autotools', '20180311'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('libgd', '2.3.0'), + ('Pango', '1.44.7'), + ('libcerf', '1.13'), + ('X11', '20200222'), + ('Qt5', '5.14.1'), + ('Lua', '5.3.5'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb new file mode 100644 index 00000000000..a8975a53237 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.10.2-GCC-9.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.10.2' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['e3b543de2f71723830a1e0472cf5489ec27d0fbeb46b1103e14a11b7177d1939'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.69.1'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a44c15f6bd1 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.4-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.6.4' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9413b8d96132d699687ef914ebb8c50440efc87b3f775d25856d7ec347c03c12'] + +builddependencies = [ + ('binutils', '2.34'), + ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.64.1'), + ('ICU', '66.1'), + ('cairo', '1.16.0'), + ('freetype', '2.10.1'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..c2e8e0f3951 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-5.6.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,33 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'hypothesis' +version = '5.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [('binutils', '2.34')] + +dependencies = [('Python', '3.8.2')] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('sortedcontainers', '2.1.0', { + 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], + }), + (name, version, { + 'checksums': ['22fb60bd0c6eb7849121a7df263a91da23b4e8506d3ba9e92ac696d2720ac0f5'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..fdbf07d08df --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('ncurses', '6.2')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..9a9385b33d5 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.24-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.24' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['44602436c52c29d4f301f55f6fd8115f945469b868348e3cddaf91ab2473ea26'] + +builddependencies = [('binutils', '2.34')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..eaf421e7afa --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +name = 'Lua' +version = '5.3.5' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..98b8cd1a8e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.4.2' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b60d58d12632ecf1e8fad7316dc82c6b9738a35625746b47ecdcaf4aed176176'] + +builddependencies = [ + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..81b1a7ee8ea --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.13-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.13' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['e4699f81af838aef5b3e77209fec8e9820a4f492d598fb5a070800854976a305'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a10f7dc9998 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.4' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20200222'), + ('Mesa', '20.0.2'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e7cf6276a3e --- /dev/null +++ b/easybuild/easyconfigs/l/libffcall/libffcall-2.2-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libffcall' +version = '2.2' + +homepage = 'https://www.gnu.org/software/libffcall/' + +description = """ + GNU Libffcall is a collection of four libraries which can be used to build + foreign function call interfaces in embedded interpreters +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ebfa37f97b6c94fac24ecf3193f9fc829517cf81aee9ac2d191af993d73cb747'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['include/avcall.h', 'include/callback.h', 'include/trampoline.h', + 'include/vacall.h', 'lib/libavcall.a', 'lib/libcallback.a', + 'lib/libtrampoline.a', 'lib/libvacall.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..140f6156f7a --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.0-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.0' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['32590e361a1ea6c93915d2448ab0041792c11bae7b18ee812514fe08b2c6a342'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('fontconfig', '2.13.92'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..11fd20dd163 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.5.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['f9e99733c170d11052f562bcd2c7cb4de53ed405f7acdde4f16195cd3ead612c'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('PROJ', '7.0.0'), + ('libjpeg-turbo', '2.0.4'), + ('zlib', '1.2.11'), + ('SQLite', '3.31.1'), + ('LibTIFF', '4.1.0'), + ('cURL', '7.69.1'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..3b9931220cc --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'https://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libmatheval-%(version)s_fix-matheval-test.patch'] +checksums = [ + '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab', # libmatheval-1.1.11.tar.gz + '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073', # libmatheval-1.1.11_fix-matheval-test.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d0a133dcfbc --- /dev/null +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.12-GCCcore-9.3.0.eb @@ -0,0 +1,26 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libsigsegv' +version = '2.12' + +homepage = 'https://www.gnu.org/software/libsigsegv/' + +description = "GNU libsigsegv is a library for handling page faults in user mode." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ae1af359eebaa4ffc5896a1aee3568c052c99879316a1ab57f8fe1789c390b6'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..63fea2c389d --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f572517667a --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.10' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """ + This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7'] + +builddependencies = [ + ('binutils', '2.34'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb new file mode 100644 index 00000000000..34040478b89 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('Perl', '5.30.2'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e869dacf3f1 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.2' + +homepage = 'https://pyyaml.org/wiki/LibYAML' + +description = """LibYAML is a YAML parser and emitter written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['4a9100ab61047fd9bd395bcef3ce5403365cafd55c1e0d0299cde14958e47be9'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cab62698e8b --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..6da88e420d0 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.0.2' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['%(name)s-%(version)s_include_float.patch'] +checksums = [ + 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 + '9e462dd578ad2a8a111983dd7fad60d08f6e481b6dd43abb12f53e5721a51364', # MPFR-4.0.2_include_float.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('GMP', '6.2.0'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2_include_float.patch b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2_include_float.patch new file mode 100644 index 00000000000..477839388df --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2_include_float.patch @@ -0,0 +1,10 @@ +Upstream patch from https://www.mpfr.org/mpfr-current/#fixed +Prepated for EasyBuild by Simon Branford (Uni. of Birmingham) +diff -Naurd mpfr-4.0.2-a/src/mpfr-impl.h mpfr-4.0.2-b/src/mpfr-impl.h +--- mpfr-4.0.2-a/src/mpfr-impl.h 2019-01-27 18:30:16.000000000 +0000 ++++ mpfr-4.0.2-b/src/mpfr-impl.h 2019-06-02 17:05:36.145226719 +0000 +@@ -57,6 +57,7 @@ + + #include + #include ++#include /* for FLT_RADIX, etc., tested below */ diff --git a/easybuild/easyconfigs/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cc0435d165f --- /dev/null +++ b/easybuild/easyconfigs/m/mbuffer/mbuffer-20191016-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'mbuffer' +version = "20191016" + +homepage = 'https://www.maier-komor.de/mbuffer.html' + +description = """ + mbuffer is a tool for buffering data streams with a large set of unique features. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.maier-komor.de/software/mbuffer'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['8dc210454765c18901074bc16e126c655135a486e73d69855caf74a157ddbe17'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/mbuffer'], + 'dirs': [], +} + +sanity_check_commands = [('mbuffer', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..868b39021a3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.4.1-GCCcore-9.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '2.4.1' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ebbe9a8e67edb4a25890b98c598e9fe23b10f96d1416d6a3ff0732e99d001c1'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': ['lib/lib%s-%%(version_major)s_%%(version_minor)s.%s' % (x, SHLIB_EXT) for x in + ['Half', 'Iex', 'IexMath', 'IlmImf', 'IlmImfUtil', 'IlmThread', 'Imath']] + + ['bin/exr%s' % x for x in + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], + 'dirs': ['include/OpenEXR', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4640d2c70a8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] + +builddependencies = [ + ('binutils', '2.34'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..7f8ef8bf517 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1e-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1e' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['694f61ac11cb51c9bf73f54e771ff6022b0327a43bbdfa1b2f19de1662a6dcbe'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.30.2'), + ('binutils', '2.34'), +] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..6b6c1bc9807 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb @@ -0,0 +1,47 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.1.5' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('libevent', '2.1.11'), + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..ad67802d6bb --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '7.0.0' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee0e14c1bd2f9429b1a28999240304c0342ed739ebaea3d4ff44c585b1097be8'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.34'), +] + +dependencies = [ + ('SQLite', '3.31.1'), + ('LibTIFF', '4.1.0'), + ('cURL', '7.69.1'), +] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..747873f9e63 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.44.7' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['66a5b6cc13db73efed67b8e933584509f8ddb7b10a8a40c3850ca4a985ea1b1f'] + +builddependencies = [ + ('binutils', '2.34'), + ('Meson', '0.53.2', '-Python-3.8.2'), + ('Ninja', '1.10.0'), + ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20200222'), + ('GLib', '2.64.1'), + ('cairo', '1.16.0'), + ('HarfBuzz', '2.6.4'), + ('FriBidi', '1.0.9'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..5131b6c1bc1 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '7.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Python', '3.8.2'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b4cfd4c12c5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.3-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '5.3' + +homepage = "https://github.com/yaml/pyyaml" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e9f45bd5b92c7974e59bcd2dcc8631a6b6cc380a904725fce7bc08872e691615'] + +builddependencies = [('binutils', '2.34')] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +dependencies = [('libyaml', '0.2.2')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..d4568e8c6c5 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'pkgconfig' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Python', '3.8.2'), + ('pkg-config', '0.29.2'), +] + +# Due to poetry doing the actual build of pkgconfig we need use_pip=False +use_pip = False + +exts_list = [ + # Not updating this since it is basically a build dep + ('poetry', '0.12.17', { + 'source_urls': ['https://pypi.python.org/packages/source/p/poetry/'], + 'checksums': ['6e535de38df7e6ab46ff8d197f53632b071675287d1477efc7bf4a5c4c63bc3f'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pkgconfig/'], + 'checksums': ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..af22457939e --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.42.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb new file mode 100644 index 00000000000..031d25a9485 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.10-GCC-9.3.0.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.10' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7b9ec5f05d61ec17bd9a82927e45d8ef37f813f79eb03fe06c88377f1bd03585'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.69.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..3fe57718257 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.1.2-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.1.2' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['SCons-3.0.4_fix-pip-install.patch'] +checksums = [ + '7801f3f62f654528e272df780be10c0e9337e897650b62ddcee9f39fde13f8fb', # scons-3.1.2.tar.gz + 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch +] + +builddependencies = [('binutils', '2.34')] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': [], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..df732575a6c --- /dev/null +++ b/easybuild/easyconfigs/s/SNPomatic/SNPomatic-1.0-GCCcore-9.3.0.eb @@ -0,0 +1,44 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'MakeCp' + +name = 'SNPomatic' +version = '1.0' + +homepage = 'https://github.com/magnusmanske/snpomatic' + +description = """ + High throughput sequencing technologies generate large amounts of short reads. + Mapping these to a reference sequence consumes large amounts of processing + time and memory, and read mapping errors can lead to noisy or incorrect + alignments. SNP-o-matic is a fast, memory-efficient, and stringent read + mapping tool offering a variety of analytical output functions, with an + emphasis on genotyping. +""" + +source_urls = ['https://github.com/magnusmanske/snpomatic/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b90123226e24edfa5c2ca296f9414b5aa005d3da77ad80b5c576adddbb38a094'] + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [('binutils', '2.34')] + +prebuildopts = "" +prebuildopts += "sed -i 's/CXX=g++/CXX:=g++/' Makefile && " +prebuildopts += "sed -i 's/CXXFLAGS=/CXXFLAGS+=/' Makefile && " +prebuildopts += "sed -i 's/LIBS=/LIBS+=/' Makefile && " +prebuildopts += 'make reassemble && make variety && make mapcontigs &&' + +local_executables = ['findknownsnps', 'reassemble', 'variety', 'mapcontigs'] + +files_to_copy = [(local_executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': [], +} + +sanity_check_commands = ['findknownsnps'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..406cb6f2d89 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.1-GCCcore-9.3.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.1' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a00b4d0d53ad97a14316135e2d702091cd5f193bb58bcfcd8bc59d41e7887a9'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('zlib', '1.2.11'), + ('PCRE', '8.44'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0416ac72d02 --- /dev/null +++ b/easybuild/easyconfigs/s/Scythe/Scythe-0.994-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'MakeCp' + +name = 'Scythe' +version = '0.994' + +homepage = 'https://github.com/ucdavis-bioinformatics/scythe' + +description = """ + Scythe uses a Naive Bayesian approach to classify contaminant substrings in + sequence reads. It considers quality information, which can make it robust in + picking out 3'-end adapters, which often include poor quality bases. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/ucdavis-bioinformatics/scythe/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['943467cbc59e7438b1db4a8e7d0e777f584ce6dbcf582053128f2924710959fc'] + +builddependencies = [('binutils', '2.34')] + +prebuildopts = "sed -i 's/CC = gcc/CC := gcc/' Makefile && " +prebuildopts += "sed -i 's/CFLAGS = -Wall/CFLAGS += -Wall/' Makefile && " + +files_to_copy = [(['scythe'], 'bin'), 'adap.fa', 'adapter_templates.txt'] + +sanity_check_paths = { + 'files': ['adap.fa', 'bin/scythe'], + 'dirs': [] +} + +sanity_check_commands = ['scythe --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..1be5caab98b --- /dev/null +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-9.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'SeqAn' +version = '2.4.0' + +homepage = 'https://github.com/seqan/seqan' + +description = """ + SeqAn is an open source C++ library of efficient algorithms and data structures + for the analysis of sequences with the focus on biological data. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/seqan/seqan/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +postinstallcmds = [ + "mkdir -p %(installdir)s/util/cmake", + "cp -a %(builddir)s/seqan-*/util/cmake/seqan-config.cmake %(installdir)s/util/cmake/", + "cp -a %(builddir)s/seqan-*/include %(installdir)s", +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", + "rabema_prepare_sam", "razers3", "seqan_tcoffee", "s4_join", "samcat", "splazers", + "yara_mapper"]] + ['util/cmake/seqan-config.cmake'], + 'dirs': ['include/seqan'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..de41bbee243 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2020.1-GCCcore-9.3.0.eb @@ -0,0 +1,18 @@ +name = 'tbb' +version = '2020.1' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7c96a150ed22bc3c6628bc3fef9ed475c00887b26d37bca61518d76a56510971'] + +builddependencies = [ + ('binutils', '2.34') +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb new file mode 100644 index 00000000000..5115e5e8314 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-9.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +dependencies = [ + ('Perl', '5.30.2'), + ('HTSlib', '1.10.2'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b3ffe5c5492 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ + +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] +builddependencies = [('binutils', '2.34')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4d858e57d89 --- /dev/null +++ b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'MakeCp' + +name = 'wtdbg2' +version = '2.5' + +homepage = 'https://github.com/ruanjue/wtdbg2' + +description = """ + Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio + or Oxford Nanopore Technologies (ONT). It assembles raw reads without error + correction and then builds the consensus from intermediate assembly output. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/ruanjue/wtdbg2/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a2ffc8503d29f491a9a38ef63230d5b3c96db78377b5d25c91df511d0df06413'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [('Perl', '5.30.2')] + +prebuildopts = "sed -i 's/CFLAGS=-g3/CFLAGS+=-g3/g' Makefile && " + +local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'pgzf'] + +files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts'], +} + +modextrapaths = { + 'PATH': 'scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/x264/x264-20191217-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20191217-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c91126155e0 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20191217-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20191217' + +homepage = 'https://www.videolan.org/developers/x264.html' + +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] +checksums = ['b2495c8f2930167d470994b1ce02b0f4bfb24b3317ba36ba7f112e9809264160'] + +builddependencies = [ + ('binutils', '2.34'), + ('NASM', '2.14.02'), +] + +configopts = " --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', + 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e03c6d0dfa7 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.3-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.3' + +homepage = 'https://x265.org/' + +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'https://bitbucket.org/multicoreware/x265/downloads/', + 'https://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f26e148ed1f4dfb33fd1eb3ff5e60e08078d1b2017e88bcbb045b3fb58300b9c'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Yasm', '1.3.0'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c493ee1fb51 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: # https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' + +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..be81e3d64a2 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.2-GCCcore-9.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.2' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebd7b5c830d6428956b67a0454a7f8cbed1de74b3b01e5c33c5378e22740f763'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.35'), +] + +configopts = '--with-pic --with-pgm --with-libsodium ' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From b964b97f75c5f524da243682a8e835b2f15713e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 08:20:00 +0200 Subject: [PATCH 262/431] add missing cURL dep for LAMMPS --- .../l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb | 1 + .../l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 1 + .../l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb | 1 + .../l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index 33114ef66ee..c4bf0a8a8dc 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -46,6 +46,7 @@ dependencies = [ ('GSL', '2.6'), ('zlib', '1.2.11'), ('gzip', '1.10'), + ('cURL', '7.66.0'), ('HDF5', '1.10.5'), ('tbb', '2019_U9'), ('PCRE', '8.43'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 8bd37bde816..68b41e024b5 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -46,6 +46,7 @@ dependencies = [ ('GSL', '2.6'), ('zlib', '1.2.11'), ('gzip', '1.10'), + ('cURL', '7.66.0'), ('HDF5', '1.10.5'), ('tbb', '2019_U9'), ('PCRE', '8.43'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index 404666e2679..d4671f247a2 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -46,6 +46,7 @@ dependencies = [ ('GSL', '2.6'), ('zlib', '1.2.11'), ('gzip', '1.10'), + ('cURL', '7.66.0'), ('HDF5', '1.10.5'), ('tbb', '2019_U9'), ('PCRE', '8.43'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index d89e7f66dc0..aef05a7fcad 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -46,6 +46,7 @@ dependencies = [ ('GSL', '2.6'), ('zlib', '1.2.11'), ('gzip', '1.10'), + ('cURL', '7.66.0'), ('HDF5', '1.10.5'), ('tbb', '2019_U9'), ('PCRE', '8.43'), From de0e82d75b280abc71ab5abb25d0c5a32d8419df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 08:53:21 +0200 Subject: [PATCH 263/431] adding easyconfigs: Boost-1.72.0-gompi-2020a.eb, Boost-1.72.0-iimpi-2020a.eb, Boost.Python-1.72.0-gompi-2020a.eb, Boost.Python-1.72.0-iimpi-2020a.eb --- .../Boost.Python-1.72.0-gompi-2020a.eb | 27 +++++++++++++++++++ .../Boost.Python-1.72.0-iimpi-2020a.eb | 27 +++++++++++++++++++ .../b/Boost/Boost-1.72.0-gompi-2020a.eb | 25 +++++++++++++++++ .../b/Boost/Boost-1.72.0-iimpi-2020a.eb | 25 +++++++++++++++++ 4 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb new file mode 100644 index 00000000000..3dcd5468ce6 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-gompi-2020a.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.72.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.71.0_fix-Python3.patch'] +checksums = [ + 'c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f', # boost_1_72_0.tar.gz + '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch +] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +dependencies = [('Boost', version)] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb new file mode 100644 index 00000000000..4ca1fb20884 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.72.0-iimpi-2020a.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.72.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.71.0_fix-Python3.patch'] +checksums = [ + 'c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f', # boost_1_72_0.tar.gz + '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch +] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +dependencies = [('Boost', version)] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb new file mode 100644 index 00000000000..9e72b168ccd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.72.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb new file mode 100644 index 00000000000..5a3becf50a6 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.72.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://dl.bintray.com/boostorg/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['c66e88d5786f2ca4dbebb14e06b566fb642a1a6947ad8cc9091f9f445134143f'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' From 4facf9f9007b25b8981b8f8d680cb6abef889c84 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 29 Apr 2020 09:28:46 +0200 Subject: [PATCH 264/431] changed deps version to match toolchain --- .../artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index cfd5da43056..c010e850d20 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -20,10 +20,10 @@ dependencies = [ ('Biopython', '1.72', versionsuffix), ('Pysam', '0.15.1', versionsuffix), ('BWA', '0.7.17'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.4', '', True), ('minimap2', '2.13'), ('SAMtools', '1.9'), - ('MUSCLE', '3.8.1551'), + ('MUSCLE', '3.8.31'), ('ETE', '3.1.1', versionsuffix), ('MAFFT', '7.427', '-with-extensions'), ('IQ-TREE', '1.6.12'), From d6d0ae163d891e8ab44a93549b178af128191409 Mon Sep 17 00:00:00 2001 From: darkless Date: Wed, 29 Apr 2020 09:30:03 +0200 Subject: [PATCH 265/431] added rampart/artic-ncov2019 exceptions --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index baa53f7d8c0..9a379523bc9 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -257,8 +257,10 @@ def check_dep_vars(self, dep, dep_vars): # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) # both scVelo and Python-Geometric depend on numba 'LLVM': (r'8\.', [r'numba-0\.47\.0-', r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']), - # medaka 0.11.4/0.12.0requires recent TensorFlow <= 1.14 (and Python 3.6) - 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-']), + # medaka 0.11.4/0.12.0requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka + 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + # rampart requires nodejs > 10, artic-ncov2019 requires rampart + 'nodejs': ('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13']), } if dep in old_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From c7a1a9852fe92a1eac026e4e0da216ca3c67c348 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 29 Apr 2020 09:59:25 +0200 Subject: [PATCH 266/431] changed MUSCLE easyconfig --- ...C-7.3.0-2.30.eb => MUSCLE-3.8.31-GCC-7.3.0-2.30.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/MUSCLE/{MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb => MUSCLE-3.8.31-GCC-7.3.0-2.30.eb} (68%) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCC-7.3.0-2.30.eb similarity index 68% rename from easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb rename to easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCC-7.3.0-2.30.eb index 6aff9d1e1c9..25e5e69d78a 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCC-7.3.0-2.30.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'MUSCLE' -version = "3.8.1551" +version = "3.8.31" homepage = 'https://drive5.com/muscle/' description = """MUSCLE is one of the best-performing multiple alignment programs @@ -12,12 +12,12 @@ description = """MUSCLE is one of the best-performing multiple alignment program toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['https://www.drive5.com/muscle/'] -sources = ['%(namelower)s_src_%(version)s.tar.gz'] +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] patches = ['%(name)s-%(version)s_fix-mk-hardcoding.patch'] checksums = [ - 'c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e', # muscle_src_3.8.1551.tar.gz - '5c38f93dcb03f769ecea7e21c83671920d0f3a88102ac6e0a51df23c33414766', # MUSCLE-3.8.1551_fix-mk-hardcoding.patch + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + 'e108d1cc2d394236f839facc1304ff96c0e11f7fdd6d2444761808ec860cd58a', # MUSCLE-3.8.31_fix-mk-hardcoding.patch ] files_to_copy = [(["muscle"], 'bin')] From 13692bfc65db4627ea1baf6d38111679ae31a6cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:01:02 +0200 Subject: [PATCH 267/431] {data}[gompi/2020a,iimpi/2020a] netCDF v4.7.4, netCDF-C++4 v4.3.1, netCDF-Fortran v4.5.2 --- .../h/HDF5/HDF5-1.10.6-iimpi-2020a.eb | 21 ++++++++++++ .../netCDF-C++4-4.3.1-gompi-2020a.eb | 25 ++++++++++++++ .../netCDF-C++4-4.3.1-iimpi-2020a.eb | 25 ++++++++++++++ .../netCDF-Fortran-4.5.2-gompi-2020a.eb | 21 ++++++++++++ .../netCDF-Fortran-4.5.2-iimpi-2020a.eb | 21 ++++++++++++ .../n/netCDF/netCDF-4.7.4-gompi-2020a.eb | 34 +++++++++++++++++++ .../n/netCDF/netCDF-4.7.4-iimpi-2020a.eb | 34 +++++++++++++++++++ 7 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb new file mode 100644 index 00000000000..0555d93603c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iimpi-2020a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.6' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb new file mode 100644 index 00000000000..751ca26705f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2020a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.7.4')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb new file mode 100644 index 00000000000..9ea1a78c17f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2020a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.7.4')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb new file mode 100644 index 00000000000..15014cc10c0 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-gompi-2020a.eb @@ -0,0 +1,21 @@ +name = 'netCDF-Fortran' +version = '4.5.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] + +dependencies = [('netCDF', '4.7.4')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb new file mode 100644 index 00000000000..2f4d520553c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.2-iimpi-2020a.eb @@ -0,0 +1,21 @@ +name = 'netCDF-Fortran' +version = '4.5.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b05c629c70d6d224a3be28699c066bfdfeae477aea211fbf034d973a8309b49'] + +dependencies = [('netCDF', '4.7.4')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020a.eb new file mode 100644 index 00000000000..e55efffd30f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-gompi-2020a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.16.4'), + ('Doxygen', '1.8.17'), +] + +dependencies = [ + ('HDF5', '1.10.6'), + ('cURL', '7.69.1'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb new file mode 100644 index 00000000000..aa9a82dfc22 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iimpi-2020a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.16.4'), + ('Doxygen', '1.8.17'), +] + +dependencies = [ + ('HDF5', '1.10.6'), + ('cURL', '7.69.1'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From 2de36180709f8a8a3dac18b02523f0429704c132 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:22:46 +0200 Subject: [PATCH 268/431] adding easyconfigs: SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb, SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb --- ...uiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb | 23 +++++++++++++++++++ ...iteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb new file mode 100644 index 00000000000..8cb1d0c786e --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-foss-2020a-METIS-5.1.0.eb @@ -0,0 +1,23 @@ +name = 'SuiteSparse' +version = '5.7.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ba5add1663d51a1b6fb128b50fe869b497f3096765ff7f8212f0ede044b9557'] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [('METIS', local_metis_ver)] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb new file mode 100644 index 00000000000..4d3b3966979 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.7.1-intel-2020a-METIS-5.1.0.eb @@ -0,0 +1,23 @@ +name = 'SuiteSparse' +version = '5.7.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ba5add1663d51a1b6fb128b50fe869b497f3096765ff7f8212f0ede044b9557'] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [('METIS', local_metis_ver)] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 79510115b58ada21a6c98a2e601bad55a9c91c47 Mon Sep 17 00:00:00 2001 From: Tardi Gradus Date: Wed, 29 Apr 2020 10:24:13 +0200 Subject: [PATCH 269/431] Update easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb index a3cbe3d6cd1..e7a4dbadf03 100644 --- a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb +++ b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb @@ -25,6 +25,7 @@ builddependencies = [ ('GtkSourceView', '3.24.11'), ('ImageMagick', '7.0.8-46'), ('MPFR', '4.0.2'), + ('cURL', '7.63.0'), ] From eb36136739ec66e12ca0e7d94575644f0c1c26f6 Mon Sep 17 00:00:00 2001 From: Tardi Gradus Date: Wed, 29 Apr 2020 10:24:23 +0200 Subject: [PATCH 270/431] Update easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb index e7a4dbadf03..74154508346 100644 --- a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb +++ b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb @@ -11,7 +11,7 @@ homepage = 'http://gretl.sourceforge.net' description = "A cross-platform software package for econometric analysis" toolchain = {'name': 'foss', 'version': '2019a'} -toolchainopts = {'openmp': True} +toolchainopts = {'openmp': True, 'usempi': True} # http://prdownloads.sourceforge.net/gretl/gretl-2020a.tar.xz source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] From b3196801f5402ac95a3d0576580dec8064f9373e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 29 Apr 2020 09:49:18 +0100 Subject: [PATCH 271/431] Fix R 3.6.3 on Power9 --- easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index a59f35b2183..68ab1f11bc9 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -2102,7 +2102,13 @@ exts_list = [ 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], }), ('liquidSVM', '1.2.4', { - 'checksums': ['15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'], + 'patches': ['liquidSVM-1.2.4-fix_ppc_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', + '21e65c8ff3f14678e43c19b4f8c36fce9bed796965abf161a147040941fc55ab', # liquidSVM-1.2.4-fix_ppc_build.patch + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], From 9d630f601d97a21625466ab9b46b64c2b79e7779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:50:33 +0200 Subject: [PATCH 272/431] add variable for commit used in artic-ncov2019 easyconfig --- .../artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index c010e850d20..de8a9ab2b28 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ easyblock = 'PythonBundle' name = 'artic-ncov2019' -# commit 4a7461c3cc9865860d69223ba8360df13a248f13 +local_commit = '4a7461c3cc9865860d69223ba8360df13a248f13' version = '2020.04.13' versionsuffix = '-Python-%(pyver)s' @@ -123,7 +123,7 @@ components = [ 'easyblock': 'Tarball', 'source_urls': ['https://github.com/artic-network/artic-ncov2019/archive/'], 'sources': [{ - 'download_filename': '4a7461c3cc9865860d69223ba8360df13a248f13.tar.gz', + 'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ, }], 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], From dff098c82fee69854270eb0cd6acd46047cb2ba7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:50:56 +0200 Subject: [PATCH 273/431] clean up commented out build dependencies in libdeflate easyconfig --- .../l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb index 4622b6cfa9d..4e7cad2274f 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb @@ -17,11 +17,7 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['45b1b2332f443b705c59d06a49be009827291d2c487b076dc8ec2791eff4c711'] -builddependencies = [ - ('binutils', '2.30'), - # ('Autotools', '20180311'), - # ('xorg-macros', '1.19.2'), -] +builddependencies = [('binutils', '2.30')] skipsteps = ['configure'] buildopts = 'PREFIX="%(installdir)s" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS"' From e62ddf85f0fcb131ad468f821bccd69762016bf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:52:16 +0200 Subject: [PATCH 274/431] add missing space in comment --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9a379523bc9..5efed20d6a8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -257,7 +257,7 @@ def check_dep_vars(self, dep, dep_vars): # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) # both scVelo and Python-Geometric depend on numba 'LLVM': (r'8\.', [r'numba-0\.47\.0-', r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']), - # medaka 0.11.4/0.12.0requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka + # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), # rampart requires nodejs > 10, artic-ncov2019 requires rampart 'nodejs': ('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13']), From 44e7d70dc1dd5c2edb0b5adbd6b854b6a0299356 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 11:48:08 +0200 Subject: [PATCH 275/431] {math,numlib}[foss/2020a,intel/2020a] PETSc v3.12.4, MUMPS v5.2.1, SCOTCH v6.0.9, Hypre v2.18.2 --- .../h/Hypre/Hypre-2.18.2-foss-2020a.eb | 18 ++++++++ .../h/Hypre/Hypre-2.18.2-intel-2020a.eb | 18 ++++++++ .../m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb | 31 +++++++++++++ .../m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb | 31 +++++++++++++ .../p/PETSc/PETSc-3.12.4-foss-2020a.eb | 44 +++++++++++++++++++ .../p/PETSc/PETSc-3.12.4-intel-2020a.eb | 44 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb | 19 ++++++++ .../s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb | 19 ++++++++ 8 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-foss-2020a.eb create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-intel-2020a.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-foss-2020a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-foss-2020a.eb new file mode 100644 index 00000000000..6075f4d2c08 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-foss-2020a.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.18.2' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-intel-2020a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-intel-2020a.eb new file mode 100644 index 00000000000..3a608227254 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.18.2-intel-2020a.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.18.2' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['28007b5b584eaf9397f933032d8367788707a2d356d78e47b99e551ab10cc76a'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb new file mode 100644 index 00000000000..849c31db3e0 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb @@ -0,0 +1,31 @@ +name = 'MUMPS' +version = '5.2.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'd988fc34dfc8f5eee0533e361052a972aa69cc39ab193e7f987178d24981744a', # MUMPS_5.2.1.tar.gz + 'e31019bedcce13acaa1867352edd99e1f67a97bb3fb7b96c7f10459c0fe301fd', # MUMPS-5.2.1_shared-pord.patch + '8973d64f44d509f1f85c6abb8b8ac9c330775f30c712f9a9e974c5541836d841', # MUMPS-5.2.1_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.0.9'), + ('METIS', '5.1.0'), +] + +parallel = 1 +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb new file mode 100644 index 00000000000..6e411ccea17 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb @@ -0,0 +1,31 @@ +name = 'MUMPS' +version = '5.2.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'd988fc34dfc8f5eee0533e361052a972aa69cc39ab193e7f987178d24981744a', # MUMPS_5.2.1.tar.gz + 'e31019bedcce13acaa1867352edd99e1f67a97bb3fb7b96c7f10459c0fe301fd', # MUMPS-5.2.1_shared-pord.patch + '8973d64f44d509f1f85c6abb8b8ac9c330775f30c712f9a9e974c5541836d841', # MUMPS-5.2.1_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.0.9'), + ('METIS', '5.1.0'), +] + +parallel = 1 +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb new file mode 100644 index 00000000000..3b8adbd8656 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb @@ -0,0 +1,44 @@ +name = 'PETSc' +version = '3.12.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +# https:// does not work here +source_urls = [ + 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3', # petsc-3.12.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Boost', '1.72.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('MUMPS', '5.2.1', '-metis'), + ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), + ('Hypre', '2.18.2'), +] + +configopts = '--LIBS="$LIBS -lrt" ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb new file mode 100644 index 00000000000..66e28a557cc --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb @@ -0,0 +1,44 @@ +name = 'PETSc' +version = '3.12.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +# https:// does not work here +source_urls = [ + 'http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3', # petsc-3.12.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Boost', '1.72.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('MUMPS', '5.2.1', '-metis'), + ('SuiteSparse', '5.7.1', '-METIS-5.1.0'), + ('Hypre', '2.18.2'), +] + +configopts = '--LIBS="$LIBS -lrt" ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb new file mode 100644 index 00000000000..34dfc411449 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.0.9' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/38187/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['622b4143cf01c480bb15708b3651b29c25e4aeb00c8c6447ff196aca2eca5c93'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb new file mode 100644 index 00000000000..c0223a3e754 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-iimpi-2020a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.0.9' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/38187/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['622b4143cf01c480bb15708b3651b29c25e4aeb00c8c6447ff196aca2eca5c93'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From 4931d6e206b21e501805be6a8929f34ee3748400 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 11:50:59 +0200 Subject: [PATCH 276/431] adding easyconfigs: IPython-7.13.0-foss-2020a-Python-3.8.2.eb, IPython-7.13.0-intel-2020a-Python-3.8.2.eb --- .../IPython-7.13.0-foss-2020a-Python-3.8.2.eb | 165 +++++++++++++++++ ...IPython-7.13.0-intel-2020a-Python-3.8.2.eb | 166 ++++++++++++++++++ 2 files changed, 331 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..30726b45662 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.13.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,165 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('ZeroMQ', '4.3.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['ca478e52ae1f88da0102360e57e528b92f3ae4316aabac80a2cd7f7ab2efb48a'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.4', { + 'checksums': ['ebe6b1b08c888b84c50d7f93dee21a09af39860144ff6130aadbd61ae8d29783'], + }), + ('ptyprocess', '0.6.0', { + 'use_pip': False, + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('traitlets', '4.3.3', { + 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], + }), + ('parso', '0.6.2', { + 'checksums': ['0c5659e0c6eba20636f99a04f469798dca8da279645ce5c387315b2c23912157'], + }), + ('jedi', '0.16.0', { + 'checksums': ['d5c871cb9360b414f981e7072c52c33258d598305280fef91c6cae34739d65d5'], + }), + ('testpath', '0.4.4', { + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('Send2Trash', '1.5.0', { + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.1.3', { + 'checksums': ['f8dfd8a7e26443e986c4e44df31870da8e906ea61096af06ba5d5cc2d519842a'], + }), + ('vcversioner', '2.16.0.0', { + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('pandocfilters', '1.4.2', { + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '19.0.0', { + 'modulename': 'zmq', + 'checksums': ['5e1f65e576ab07aed83f444e201d86deb01cd27dcf3f37c727bc8729246a60a8'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('nbformat', '5.0.4', { + 'checksums': ['562de41fc7f4f481b79ab5d683279bf3a168858268d4387b489b7b02be0b324a'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('nbconvert', '5.6.1', { + 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], + }), + ('terminado', '0.8.3', { + 'use_pip': False, + 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], + }), + ('tornado', '6.0.4', { + 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], + }), + ('jupyter_client', '6.1.0', { + 'checksums': ['61429e7d2c4b385135d31054944dd3f23a1c6affb0ca3d4328d42fc9ba82b7f5'], + }), + ('backcall', '0.1.0', { + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '5.2.0', { + 'checksums': ['37c65d2e2da3326e5cf114405df6d47d997b8a3eba99e2cc4b75833bf71a5e18'], + }), + ('prometheus_client', '0.7.1', { + 'checksums': ['71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da'], + }), + ('pyrsistent', '0.15.7', { + 'checksums': ['cdc7b5e3ed77bed61270a47d35434a30617b9becdf2478af76ad2c6ade307280'], + }), + ('ipywidgets', '7.5.1', { + 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], + }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), + ('jupyter_nbextensions_configurator', '0.4.1', { + 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], + }), + ('notebook', '6.0.3', { + 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('ipympl', '0.5.6', { + 'checksums': ['076240e606f4dc1f23b7ecc3303c759f5718dc16f9a119382776c6cb382a53e9'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..663b4833150 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.13.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,166 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.13.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('ZeroMQ', '4.3.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator +] + +use_pip = True +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['ca478e52ae1f88da0102360e57e528b92f3ae4316aabac80a2cd7f7ab2efb48a'], + }), + ('pexpect', '4.8.0', { + 'checksums': 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{ + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('Send2Trash', '1.5.0', { + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.1.3', { + 'checksums': ['f8dfd8a7e26443e986c4e44df31870da8e906ea61096af06ba5d5cc2d519842a'], + }), + ('vcversioner', '2.16.0.0', { + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('pandocfilters', '1.4.2', { + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '19.0.0', { + 'modulename': 'zmq', + 'checksums': ['5e1f65e576ab07aed83f444e201d86deb01cd27dcf3f37c727bc8729246a60a8'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('nbformat', '5.0.4', { + 'checksums': ['562de41fc7f4f481b79ab5d683279bf3a168858268d4387b489b7b02be0b324a'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('nbconvert', '5.6.1', { + 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], + }), + ('terminado', '0.8.3', { + 'use_pip': False, + 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], + }), + ('tornado', '6.0.4', { + 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], + }), + ('jupyter_client', '6.1.0', { + 'checksums': ['61429e7d2c4b385135d31054944dd3f23a1c6affb0ca3d4328d42fc9ba82b7f5'], + }), + ('backcall', '0.1.0', { + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '5.2.0', { + 'checksums': ['37c65d2e2da3326e5cf114405df6d47d997b8a3eba99e2cc4b75833bf71a5e18'], + }), + ('prometheus_client', '0.7.1', { + 'checksums': ['71cd24a2b3eb335cb800c7159f423df1bd4dcd5171b234be15e3f31ec9f622da'], + }), + ('pyrsistent', '0.15.7', { + 'checksums': ['cdc7b5e3ed77bed61270a47d35434a30617b9becdf2478af76ad2c6ade307280'], + }), + ('ipywidgets', '7.5.1', { + 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], + }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), + ('jupyter_nbextensions_configurator', '0.4.1', { + 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], + }), + ('notebook', '6.0.3', { + 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('ipympl', '0.5.6', { + 'checksums': ['076240e606f4dc1f23b7ecc3303c759f5718dc16f9a119382776c6cb382a53e9'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' From 531c8ff77a669238f2b8d4ad7380f52dfd74d284 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 29 Apr 2020 12:00:27 +0200 Subject: [PATCH 277/431] adding easyconfigs: HDF-EOS-2.20-GCCcore-7.3.0.eb --- .../h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..34d17fa122e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS' +version = '2.20' + +homepage = 'http://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/latest_release/', + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/previous_releases/', +] + +sources = ['%(name)s%(version)sv1.00.tar.Z'] + +checksums = ['cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903'] + +builddependencies = [ + ('binutils', '2.30'), +] + +dependencies = [ + ('HDF', '4.2.14'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF/bin/h4cc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HdfEosDef.h', 'include/HDFEOSVersion.h', 'lib/libGctp.la', 'lib/libhdfeos.la'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From 1409b991a43ceaf9653eab587eb5ce00cd42f144 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 29 Apr 2020 12:16:15 +0200 Subject: [PATCH 278/431] update extension list in R-4.0.0-foss-2020a.eb --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 387 +++++++++--------- 1 file changed, 193 insertions(+), 194 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 81ff1b42e7d..daac80e76be 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -69,7 +69,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 25 March 2020 +# packages updated on 29 April 2020 exts_list = [ 'base', 'datasets', @@ -91,8 +91,8 @@ exts_list = [ ('magic', '1.5-9', { 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], }), - ('Rcpp', '1.0.4', { - 'checksums': ['d992fe8f7480606a0790be94948a6b667f37aa607ccd5e5613e88af861bb00d5'], + ('Rcpp', '1.0.4.6', { + 'checksums': ['45af675ddbbe155e671453b2e84fe32250bb98d4ccb4342b61c1e25cff10b302'], }), ('RcppProgress', '0.4.2', { 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], @@ -112,8 +112,8 @@ exts_list = [ ('filehash', '2.4-2', { 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], }), - ('ff', '2.2-14', { - 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], + ('ff', '2.2-14.2', { + 'checksums': ['f8c06ac333ffe3545cdf56531619865176e1827728f7aeeba82d135d5c5e37e4'], }), ('bnlearn', '4.5', { 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], @@ -133,8 +133,8 @@ exts_list = [ ('formatR', '1.7', { 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], }), - ('gtools', '3.8.1', { - 'checksums': ['051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38'], + ('gtools', '3.8.2', { + 'checksums': ['503ba60a41f3c61b8129c25de62c74dab29761d2e661d4addd106e2e02f1dcde'], }), ('gdata', '2.18.0', { 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], @@ -160,8 +160,8 @@ exts_list = [ ('mime', '0.9', { 'checksums': ['2ccf97d2940a09539dc051c7a9a1aee90ef04b34e9bc6c0b64b4435fb3c2fa80'], }), - ('xfun', '0.12', { - 'checksums': ['ae0d3312b3642d1748a6773debb43b18d57b04f2345c562b7da1a7e8d444f069'], + ('xfun', '0.13', { + 'checksums': ['a3da8d53b74ae58bb0f121177dcf3caf312c65fc181c18f168abd59afac33e0e'], }), ('markdown', '1.1', { 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], @@ -172,8 +172,8 @@ exts_list = [ ('NLP', '0.2-0', { 'checksums': ['fc64c80124c4e53b20f92b60c68e2fd33ee189653d0ceea410c32dd66d9e7075'], }), - ('mclust', '5.4.5', { - 'checksums': ['75f2963082669485953e4306ffa93db98335ee6afdc1318b95d605d56cb30a72'], + ('mclust', '5.4.6', { + 'checksums': ['d4ffcf36bf709ad42dccb2387263f67ca32012b0707f0ef6eda32730b5c286fc'], }), ('RANN', '2.6.1', { 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], @@ -208,14 +208,14 @@ exts_list = [ ('ADGofTest', '0.3', { 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), - ('MASS', '7.3-51.5', { - 'checksums': ['464c0615cef01820cde2bb8457e81575d6755ae9b3ac99f3bfaaac47d43d15cc'], + ('MASS', '7.3-51.6', { + 'checksums': ['e2035c47d8428b52afc02dd4f87ccb39a0085629932dfaff5f0a5d2c84ef3eee'], }), ('pixmap', '0.4-11', { 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], }), - ('lattice', '0.20-40', { - 'checksums': ['d594ed6928101873c30c0abad12d25613a43e84d0e3742b68bfa27dfbed3a3f0'], + ('lattice', '0.20-41', { + 'checksums': ['54ca557f0cb33df60eb10b883c2ed2847e061ddd57ed9b5dd7695149609d57b5'], }), ('sp', '1.4-1', { 'checksums': ['8f96f1a4827eea2cc02bb35c418ce2bdaf2d5ea47a214bcd4bc85f928b417039'], @@ -244,8 +244,8 @@ exts_list = [ ('longitudinal', '1.1.12', { 'checksums': ['d4f894c38373ba105b1bdc89e3e7c1b215838e2fb6b4470b9f23768b84e603b5'], }), - ('backports', '1.1.5', { - 'checksums': ['63ec38adf383b70b4cd2b661ad353afacff9c4388353578bf4302ab190e1294c'], + ('backports', '1.1.6', { + 'checksums': ['d0e8af477514d81b46cc777e0fa532835c1dc7eecd3c2432bb40228131bc199c'], }), ('checkmate', '2.0.0', { 'checksums': ['0dc25b0e20c04836359df1885d099c6e4ad8ae0e585a9e4107f7ea945d9c6fa4'], @@ -292,8 +292,8 @@ exts_list = [ ('magrittr', '1.5', { 'checksums': ['05c45943ada9443134caa0ab24db4a962b629f00b755ccf039a2a2a7b2c92ae8'], }), - ('glue', '1.3.2', { - 'checksums': ['6f3452efb571a0ada8767356e33df67794b2dd514792ab35637522e318a6932a'], + ('glue', '1.4.0', { + 'checksums': ['ea6c409f7141754baa090deba96cff270a11b185452cf9e6fb69cb148a9069c1'], }), ('stringr', '1.4.0', { 'checksums': ['87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd'], @@ -310,8 +310,8 @@ exts_list = [ ('permute', '0.9-5', { 'checksums': ['d2885384a07497e8df273689d6713fc7c57a7c161f6935f3572015e16ab94865'], }), - ('plotrix', '3.7-7', { - 'checksums': ['a4e8ebda8560ad613b9320d39673879f302da791ac3293ff3f22f8ec7cad22f5'], + ('plotrix', '3.7-8', { + 'checksums': ['8ccd1f7e656413b9956cea614c986ce9cc61366deba356afb38cee6672a59480'], }), ('randomForest', '4.6-14', { 'checksums': ['f4b88920419eb0a89d0bc5744af0416d92d112988702dc726882394128a8754d'], @@ -325,11 +325,11 @@ exts_list = [ ('tripack', '1.3-9', { 'checksums': ['2b40670c23894b12e86a36fb2f42cab4728c8af8bd5338e94fbf86b7916a8c10'], }), - ('irace', '3.3', { - 'checksums': ['4442d968d2201194555eef69f7fbd986a3c553dd6f2f63a26415168c280b0d10'], + ('irace', '3.4.1', { + 'checksums': ['7eea92ba42e6ba320fa8bdca3c53091ae42f26a0f097244f65e7e117f6d514b6'], }), - ('rJava', '0.9-11', { - 'checksums': ['c28ae131456a98f4d3498aa8f6eac9d4df48727008dacff1aa561fc883972c69'], + ('rJava', '0.9-12', { + 'checksums': ['2248a8c73cacfecf75445ad0ebda4960409ec3f21afb180a1bc02a6de4057b0f'], }), ('RColorBrewer', '1.1-2', { 'checksums': ['f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd'], @@ -346,8 +346,8 @@ exts_list = [ ('Matrix', '1.2-18', { 'checksums': ['f7ff018c2811946767ffd4c96d3987e859b82786ff72e1c211ab18bc03cb6119'], }), - ('RcppArmadillo', '0.9.850.1.0', { - 'checksums': ['9fcb28335e94c308dc5cd8c348a7a02c4b7bea11a87498e121f072be2aa42c61'], + ('RcppArmadillo', '0.9.870.2.0', { + 'checksums': ['bb605d6702d49d447b18986d9a7864b27e5512630a6713bca67afbb5bb54f1e4'], }), ('plyr', '1.8.6', { 'checksums': ['ea55d26f155443e9774769531daa5d4c20a0697bb53abd832e891b126c935287'], @@ -355,8 +355,8 @@ exts_list = [ ('gtable', '0.3.0', { 'checksums': ['fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3'], }), - ('reshape2', '1.4.3', { - 'checksums': ['8aff94c935e75032344b52407593392ddd4e16a88bb206984340c816d42c710e'], + ('reshape2', '1.4.4', { + 'checksums': ['d88dcf9e2530fa9695fc57d0c78adfc5e361305fe8919fe09410b17da5ca12d8'], }), ('dichromat', '2.0-0', { 'checksums': ['31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1'], @@ -418,17 +418,17 @@ exts_list = [ ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), - ('tibble', '2.1.3', { - 'checksums': ['9a8cea9e6b5d24a7e9bf5f67ab38c40b2b6489eddb0d0edb8a48a21ba3574e1a'], + ('tibble', '3.0.1', { + 'checksums': ['154552cfb767e0bd48ef3fc61df8286ce52205e970815c5bc2560f41eceea79e'], }), ('lazyeval', '0.2.2', { 'checksums': ['d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4'], }), - ('withr', '2.1.2', { - 'checksums': ['41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686'], + ('withr', '2.2.0', { + 'checksums': ['4c21e51cf48f8c281ddd5f5ec358ac446df3c982104fd00bfe62d9259d73b582'], }), - ('nlme', '3.1-145', { - 'checksums': ['30f3d8caa77b9ff46af2d56758d3fac026af1290e0d708f48c5fd8da9c1a2ac5'], + ('nlme', '3.1-147', { + 'checksums': ['efc8d82e5758c4696458f647f2b8bb1776fdbff6c8eaad3fe3c0573a3c1f0ce7'], }), ('mgcv', '1.8-31', { 'checksums': ['736de462a0ac43a6ed38cd57dfb0ba2942c941dfbb538128782727ab7125c3c5'], @@ -445,14 +445,14 @@ exts_list = [ ('processx', '3.4.2', { 'checksums': ['94a0ffc632759be85d13b7b11ed006adf6c08c2d9cd99612cd0372833bd75c09'], }), - ('callr', '3.4.2', { - 'checksums': ['cca155a38474c55906a9eaa58d4ae6fff0facf13926a2ccda0cef3a528b8b42d'], + ('callr', '3.4.3', { + 'checksums': ['01b7277f20c1d662c6bebbfa2798d179922b36d4148b4298853579aeda0382b5'], }), ('prettyunits', '1.1.1', { 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], }), - ('pkgbuild', '1.0.6', { - 'checksums': ['bd736cadcb9938df9fafddd362f9f032934a93b9853b981eb3754db8a3f9d476'], + ('pkgbuild', '1.0.7', { + 'checksums': ['29bb38a38202ba780d2d46aeca0a6e2f052653e4a83891ec38d19bebd131a971'], }), ('rstudioapi', '0.11', { 'checksums': ['13e07fb7e2eba8cf1d885db2721901d676d219a1042d7ef5d166125e4905306b'], @@ -466,14 +466,14 @@ exts_list = [ ('testthat', '2.3.2', { 'checksums': ['1a268d8df07f7cd8d282d03bb96ac2d96a24a95c9aa52f4cca5138a09dd8e06c'], }), - ('isoband', '0.2.0', { - 'checksums': ['783197e50c0a58ada4f8b5980d52150264eaab4fd97e14faddf67a3c8e1e02e4'], + ('isoband', '0.2.1', { + 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], }), ('ggplot2', '3.3.0', { 'checksums': ['320e3c76fe0d0397e29f4782bf85af3647518154b3900a39fd18cf024c554148'], }), - ('pROC', '1.16.1', { - 'checksums': ['35bd783811ba0138a1f8d6d7eecca7fc3c98f7aec62fe094ea577741fd0a7762'], + ('pROC', '1.16.2', { + 'checksums': ['b68b960ed9a2cdea7976943649082c3945e370d14115b7adbce440fc7f51fc2a'], }), ('quadprog', '1.5-8', { 'checksums': ['22128dd6b08d3516c44ff89276719ad4fe46b36b23fdd585274fa3a93e7a49cd'], @@ -499,14 +499,14 @@ exts_list = [ ('pls', '2.7-2', { 'checksums': ['67e91e36dbebeb2f2d9c9b88f310dc00f70de275e5f382f392e72dd36af42b88'], }), - ('class', '7.3-15', { - 'checksums': ['f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4'], + ('class', '7.3-17', { + 'checksums': ['be1f85b6df7556db93f50cb08106aac6620d4b5bb3fee846422863a022461313'], }), ('e1071', '1.7-3', { 'checksums': ['bb2dba526b673ec3a573befe365e3500b773593f0384fd6694e0835496bcc25d'], }), - ('nnet', '7.3-13', { - 'checksums': ['ae8820e292c7a413206ef82d1f41da2809c1d0e39c97f6800f9c7952599119fc'], + ('nnet', '7.3-14', { + 'checksums': ['5d1b9e9764d74d16c651f18f949aa4e9e2995ba64633cbfa2c6a7355ae30f4af'], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -517,11 +517,11 @@ exts_list = [ ('MatrixModels', '0.4-1', { 'checksums': ['fe878e401e697992a480cd146421c3a10fa331f6b37a51bac83b5c1119dcce33'], }), - ('quantreg', '5.54', { - 'checksums': ['703b2c67d88e95eaf1bf3c09fc64c1964bcc1145244c8bc8c0e5ac99713ad0a6'], + ('quantreg', '5.55', { + 'checksums': ['cbe1541409aed8222a41043958ab9c352b84dba4e0766b54bf1eac59d2454cfe'], }), - ('robustbase', '0.93-5', { - 'checksums': ['bde564dbd52f04ab32f9f2f9dd09b9578f3ccd2541cf5f8ff430da42a55e7f56'], + ('robustbase', '0.93-6', { + 'checksums': ['ea1463a646a0aad0cc6f48e011c8baf990178f1228e0759be63259123b3a24b3'], }), ('zoo', '1.8-7', { 'checksums': ['9e072ddc8f245adcdeb230cbf0c818db9c028c320894f48211758da2bf2085f0'], @@ -529,8 +529,8 @@ exts_list = [ ('lmtest', '0.9-37', { 'checksums': ['ddc929f94bf055974832fa4a20fdd0c1eb3a84ee11f716c287936f2141d5ca0a'], }), - ('vcd', '1.4-6', { - 'checksums': ['7f804081a722e98885c4bc8b57be67486ffa3dcb681a5ea3b2dcd0e26f225f66'], + ('vcd', '1.4-7', { + 'checksums': ['ec89b2ad202b89d70344b49d9410ddc8a15dced00462ed7e6f9b516811325299'], }), ('snowfall', '1.84-6.1', { 'checksums': ['5c446df3a931e522a8b138cf1fb7ca5815cc82fcf486dbac964dcbc0690e248d'], @@ -538,8 +538,8 @@ exts_list = [ ('rpart', '4.1-15', { 'checksums': ['2b8ebe0e9e11592debff893f93f5a44a6765abd0bd956b0eb1f70e9394cfae5c'], }), - ('survival', '3.1-11', { - 'checksums': ['44f6120ff977ac576b8fa15c0626dfef8d80ba392dc03364b5e15dbb465d70b9'], + ('survival', '3.1-12', { + 'checksums': ['b62ed66eb646f3df13f7e9bf6571e3bfecae128c66491e174c8833cbef1bf21f'], }), ('bindr', '0.1.1', { 'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'], @@ -550,8 +550,8 @@ exts_list = [ ('bindrcpp', '0.2.2', { 'checksums': ['48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467'], }), - ('purrr', '0.3.3', { - 'checksums': ['0f31a89a424e12e35bd6e0581dee1d160f1f8be1f0a883a7d33ccbde8ef69e9e'], + ('purrr', '0.3.4', { + 'checksums': ['23ebc93bc9aed9e7575e8eb9683ff4acc0270ef7d6436cc2ef4236a9734840b2'], }), ('tidyselect', '1.0.0', { 'checksums': ['fe761766d03af86d04da9a9a7800e9c8271d2cb067776cfb817d853725d59caf'], @@ -565,9 +565,8 @@ exts_list = [ ('mnormt', '1.5-6', { 'checksums': ['2951fcc9711d577d7d5577d313875c4ed9f7a7a06df8c3b62fa27c231f021e4d'], }), - ('foreign', '0.8-76', { - 'checksums': [('052e580bc1e1334b41e7d693df341858395e72488d9c4b3ed8968bf04317ddfc', - '8bdc9337345d9126e5882f0d1538eb714c3e39a40b78b53a73271adc8fa9625d')], + ('foreign', '0.8-79', { + 'checksums': ['af36b6945afbf849543ef7e432e27fecb66d5a8b3932b2428e59c2392699b9b4'], }), ('psych', '1.9.12.31', { 'checksums': ['25e71dbe0b0d8211e7a9c8439c1c205a25fd571a0f95a89b8425b87b95b9290a'], @@ -575,17 +574,17 @@ exts_list = [ ('generics', '0.0.2', { 'checksums': ['71b3d1b719ce89e71dd396ac8bc6aa5f1cd99bbbf03faff61dfbbee32fec6176'], }), - ('broom', '0.5.5', { - 'checksums': ['dda5213bcb756fee729310ca4dea6000289dfb12342311db566e0e238869ff58'], + ('broom', '0.5.6', { + 'checksums': ['0b06f670ace7349b95a71313c360dbded2428d65d17eaacccc93750196964335'], }), ('nloptr', '1.2.2.1', { 'checksums': ['d037bea484725cf6cbc069eee17db17f1bc8fc4edc1f1ca16cf6c34bc21610ae'], }), - ('boot', '1.3-24', { - 'checksums': ['89d4596d4a1287155597257372a872b04fbd406cd23fd8436f8e56394ba1607b'], + ('boot', '1.3-25', { + 'checksums': ['464835fcb453072346ce49e4ae318e04c9dba682349be49db616623b6088fbbe'], }), - ('lme4', '1.1-21', { - 'checksums': ['7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c'], + ('lme4', '1.1-23', { + 'checksums': ['99d542b1f78fae33a64f1b8eec33b7a4532a8d82d2ac47bdb2838248f14c0262'], }), ('ucminf', '1.1-4', { 'checksums': ['a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07'], @@ -653,8 +652,8 @@ exts_list = [ ('codetools', '0.2-16', { 'checksums': ['f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501'], }), - ('foreach', '1.4.8', { - 'checksums': ['ac3ce7e4bd603fb0ae2728c2f9fc379ad4540d636fb71125405c18ee042d8ef7'], + ('foreach', '1.5.0', { + 'checksums': ['1af9a713418c4cdeb49c4194f6482a7ee8ae4959b995a958a8a8a19ec8b60415'], }), ('doMC', '1.3.6', { 'checksums': ['2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2'], @@ -680,8 +679,8 @@ exts_list = [ ('hwriter', '1.3.2', { 'checksums': ['6b3531d2e7a239be9d6e3a1aa3256b2745eb68aa0bdffd2076d36552d0d7322b'], }), - ('KernSmooth', '2.23-16', { - 'checksums': ['b8c251fea1483a8ade005faf31dff9d85d2b6da08dcd661bf1e4a861db9a99a9'], + ('KernSmooth', '2.23-17', { + 'checksums': ['2b3d73fe15db46dbc2f6e3b043baadb7633c46bfa4a66d9eea5aed633058e685'], }), ('xts', '0.12-0', { 'checksums': ['df11e6dad7cf0a266702988fa6127aaf72437da743ca40e9abcd9e6b3d628c60'], @@ -692,8 +691,8 @@ exts_list = [ ('TTR', '0.23-6', { 'checksums': ['afc10a89d3a18f121ddf0f7256408eeb05cc64e18ee94e654bfa803e5415e265'], }), - ('quantmod', '0.4-16', { - 'checksums': ['826de2c821799cf9ced09d99d277d91aeb74eec75b5a89fb533ee4a5505e858a'], + ('quantmod', '0.4.17', { + 'checksums': ['0aff56f276f8e347c56356060f7320913f0e417f1c5411c49f0865ca732044eb'], }), ('mvtnorm', '1.1-0', { 'checksums': ['8112e12eb11f5db2ff145893f48426520e669be99b87889457dd2c4f2636cb5d'], @@ -734,14 +733,14 @@ exts_list = [ ('sandwich', '2.5-1', { 'checksums': ['dbef6f4d12b83e166f9a2508b7c732b04493641685d6758d29f3609e564166d6'], }), - ('sfsmisc', '1.1-5', { - 'checksums': ['8e22efffce0df5dc84b53445b9f5d225a59d057ba90fe608299d20bb447d789c'], + ('sfsmisc', '1.1-6', { + 'checksums': ['57b22cdd713e71e9235ff1ace8cdf73564bfdcee4b018f3d7cde6fb35493db11'], }), - ('spatial', '7.3-11', { - 'checksums': ['624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11'], + ('spatial', '7.3-12', { + 'checksums': ['7639039ee7407bd088e1b253376b2cb4fcdf4cc9124d6b48e4119d5cda872d63'], }), - ('VGAM', '1.1-2', { - 'checksums': ['f8071339f127121945954c98168749efcc179c67c70437d35b5d684fd4b0ca4f'], + ('VGAM', '1.1-3', { + 'checksums': ['0c9ff51b9ee76d8b182a19b61f278970ad6d421c0206bfef40b7413b7acb94c3'], }), ('waveslim', '1.8.2', { 'checksums': ['133c4f7a027282742fe99b583ca65f178fc7a3df2ce75cb4d60650f0a1dd7145'], @@ -833,8 +832,8 @@ exts_list = [ ('htmlTable', '1.13.3', { 'checksums': ['d459c43675f6ee0a1ae8232ea8819b2a842e795a833b28127081fa344d09393d'], }), - ('Hmisc', '4.3-1', { - 'checksums': ['8cb371eb25bd4afc294edd564d30cf52632bfa5907f4c52e62b53195c239d10a'], + ('Hmisc', '4.4-0', { + 'checksums': ['f16ecf4c5ee2202d51f426282a54f8000ffa8b9747c3e910205f34f878556ec7'], }), ('fastcluster', '1.1.25', { 'checksums': ['f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205'], @@ -917,17 +916,17 @@ exts_list = [ ('expm', '0.999-4', { 'checksums': ['58d06427a08c9442462b00a5531e2575800be13ed450c5a1546261251e536096'], }), - ('raster', '3.0-12', { - 'checksums': ['6f3750f226a3257a71274bf490378f54ff7498ced678ea108b4d773c5fd42b67'], + ('raster', '3.1-5', { + 'checksums': ['db6622d55bb9e5c4a8d8e59887a802b35fc07dcee946800453bc5e1901c01a04'], }), - ('spData', '0.3.3', { - 'checksums': ['85fa747e358528386216394af6fb717642703d3067a3c3cadef09caef7c4c6ec'], + ('spData', '0.3.5', { + 'checksums': ['901e840ba42e945d51ea0dfe815fece44dd92a8e74a2356345ccbb2577908926'], }), ('units', '0.6-6', { 'checksums': ['d0b6c76afb9aa5d7a0eaae05e6fc1bd2bb9d62d4c43e986b4782d6e5c2efa687'], }), - ('classInt', '0.4-2', { - 'checksums': ['bb0da1e7db779831cf5cea80722ade90bf83a9aa51b7d2bc6bee69c433042871'], + ('classInt', '0.4-3', { + 'checksums': ['9ede7a2a7a6b6c114919a3315a884fb592e33b037a50a4fe45cbd4fe2fc434ac'], }), ('vegan', '2.5-6', { 'checksums': ['b3c00aceb3db38101960515658e2b9ec1552439c3ed4e26e72989f18eccbc03c'], @@ -941,8 +940,8 @@ exts_list = [ ('XML', '3.99-0.3', { 'checksums': ['81b7a76308f3b7378dff525eff0180bba73b31117483a26cc3aa172d15c7f753'], }), - ('tinytex', '0.20', { - 'checksums': ['6f6e57d41d8057c17a864004ae6587a95ac3288672e16d35c829317d6d441b59'], + ('tinytex', '0.22', { + 'checksums': ['6bbcbc907cad14bc0a583670bad1d9648d1f1cedd364354042aee83bb6302e69'], }), ('rmarkdown', '2.1', { 'checksums': ['ef450e21206c454aa78eeca9023bbc78d1b2939e0b4bed9fdec9f2bf81ee455d'], @@ -950,8 +949,8 @@ exts_list = [ ('reshape', '0.8.8', { 'checksums': ['4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168'], }), - ('xml2', '1.2.5', { - 'checksums': ['24611fcc0bc15761158a92d880ea2bcd74962b987283f040c0ee0f8dde0be656'], + ('xml2', '1.3.2', { + 'checksums': ['df22f9e7e3189d8c9b8804eaf0105324fdac983cffe743552f6d76613600a4cf'], }), ('triebeard', '0.3.0', { 'checksums': ['bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3'], @@ -959,8 +958,8 @@ exts_list = [ ('urltools', '1.7.3', { 'checksums': ['6020355c1b16a9e3956674e5dea9ac5c035c8eb3eb6bbdd841a2b5528cafa313'], }), - ('httpcode', '0.2.0', { - 'checksums': ['fbc1853db742a2cc1df11285cf27ce2ea43bc0ba5f7d393ee96c7e0ee328681a'], + ('httpcode', '0.3.0', { + 'checksums': ['593a030a4f94c3df8c15576837c17344701bac023ae108783d0f06c476062f76'], }), ('crul', '0.9.0', { 'checksums': ['a7b42c69ca31648a419b93c618d32d0613f3ea053e45d584e84ef422ccf531c0'], @@ -980,14 +979,14 @@ exts_list = [ ('solrium', '1.1.4', { 'checksums': ['5fccdb455746493c56e4df91f01ea9e89cdf0d67cfa5f958ca246b9207d20375'], }), - ('ritis', '0.8.0', { - 'checksums': ['23bc11599a64c25fe7a60e86fa3cd8c4078e140bc338c6d51d8d75b81564ecbd'], + ('ritis', '0.9.0', { + 'checksums': ['4abbe6c860fd3e465116573c9b2f119dbbd0046646844551523188ded63f0f6c'], }), ('worrms', '0.4.0', { 'checksums': ['8480c56a4412662a383103fef68e73fcf14e94fcb878c25df8c6d5a8c0146059'], }), - ('natserv', '0.3.0', { - 'checksums': ['3c207d45bbba75dfd16f40d6eaaac122e40b3d3ca05b3b98aa8ed3c092638e5e'], + ('natserv', '0.4.0', { + 'checksums': ['ba7ef96290b4713e46197cc872d5400710086dc3668717d67995ee3de3d19c87'], }), ('WikipediR', '1.5.0', { 'checksums': ['f8d0e6f04fb65f7ad9c1c068852a6a8b699ffe8d39edf1f3fa07d32d087e8ff0'], @@ -1001,8 +1000,8 @@ exts_list = [ ('phangorn', '2.5.5', { 'checksums': ['c58dc1ace26cb4358619a15da3ea4765dbdde1557acccc5103c85589a7571346'], }), - ('taxize', '0.9.92', { - 'checksums': ['7409de8a860b6d6452d19e6b53d37b7d49008f2d221e2bb1b5fb7fbe991f6f71'], + ('taxize', '0.9.95', { + 'checksums': ['8a27d81678e60f67082d9b0b3cd104fe531ea2be2d9073a20cab016259228834'], }), ('uuid', '0.1-4', { 'checksums': ['98e0249dda17434bfa209c2058e9911e576963d4599be9f7ea946e664f8ca93e'], @@ -1049,8 +1048,8 @@ exts_list = [ ('shapefiles', '0.7', { 'checksums': ['eeb18ea4165119519a978d4a2ba1ecbb47649deb96a7f617f5b3100d63b3f021'], }), - ('fossil', '0.3.7', { - 'checksums': ['3feba6ceecaa6f2f68fdc1ceb0019395ccfadb0cf033e1709dddb690c7f210a1'], + ('fossil', '0.4.0', { + 'checksums': ['37c082fa15ebae89db99d6071b2bb2cad6a97a0405e9b4ef77f62a8f6ad274c1'], }), ('geiger', '2.0.6.4', { 'checksums': ['8ddc12779b86b14b173a5c72a28c4e22784e4a7a48e6c806e48a097c2928af64'], @@ -1073,8 +1072,8 @@ exts_list = [ ('manipulateWidget', '0.10.1', { 'checksums': ['9d621192121f6b516bc7f1a18305995bfb7838c6683ac701422afc03a50e27ee'], }), - ('rgl', '0.100.50', { - 'checksums': ['5e9d90770018c5adc0dbbe5440633259f5c6ca3d84fd40ea94b71d5ac548b798'], + ('rgl', '0.100.54', { + 'checksums': ['17b7f8f135f526aba17dc516952f692daa7a7d6e787157fdff8dd5175113fad5'], }), ('Rtsne', '0.15', { 'checksums': ['56376e4f0a382fad3d3d40e2cb0562224be5265b827622bcd235e8fc63df276c'], @@ -1094,8 +1093,8 @@ exts_list = [ ('TH.data', '1.0-10', { 'checksums': ['618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55'], }), - ('multcomp', '1.4-12', { - 'checksums': ['0b38a7ad703b78dbdf0956a1c1e22bd21fd02c3799b8e2e9e186949f41708291'], + ('multcomp', '1.4-13', { + 'checksums': ['d30f0357b8307e7feb574d6d307e0ebc6bdca66b2cc172980fa5309685885fdb'], }), ('libcoin', '1.0-5', { 'checksums': ['0a744164e00557d2f3e888d14cfd6108d17c14e983db620f74c7a5475be8a9b2'], @@ -1148,8 +1147,8 @@ exts_list = [ ('tm', '0.7-7', { 'checksums': ['d0dbe41ff8414bdc2eee06a1b0d6db4567850135c4c6ff0a9c9ca8239166d15f'], }), - ('TraMineR', '2.0-15', { - 'checksums': ['fb9f5bf7bb26d0abcffaa1bd917d4d8bcc134fcbc4e8834fbbaff83fdbcacf79'], + ('TraMineR', '2.2-0', { + 'checksums': ['eeaeaf5151ec7a6b7179fd04dbdfb16479b4893e1547ccc29be74e444691d0f6'], }), ('chemometrics', '1.4.2', { 'checksums': ['b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a'], @@ -1184,11 +1183,11 @@ exts_list = [ ('gsalib', '2.1', { 'checksums': ['e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc'], }), - ('optparse', '1.6.4', { - 'checksums': ['cd7855ebc2303da4ab0615282667c7eeef5329faf51bd2bf2e4b0d250561d973'], + ('optparse', '1.6.6', { + 'checksums': ['51779d497146e9354b1153713d939e81551e08948c2b00e4b117b1377c0b60d0'], }), - ('labelled', '2.2.2', { - 'checksums': ['0616197cc3ceadd45b6967497aee7d53b87c8b719ff54b033e31a70fd61c48c3'], + ('labelled', '2.3.0', { + 'checksums': ['9f16f168436039d7881d535a9f15fb0dce752fd3a28bce89192718cdbd043a50'], }), ('questionr', '0.7.0', { 'checksums': ['c4566880a1ca8f01faad396e20d907d913f4a252acaf83a0cb508a3738874cb3'], @@ -1199,11 +1198,11 @@ exts_list = [ ('neuRosim', '0.2-12', { 'checksums': ['f4f718c7bea2f4b61a914023015f4c71312f8a180124dcbc2327b71b7be256c3'], }), - ('locfit', '1.5-9.1', { - 'checksums': ['f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51'], + ('locfit', '1.5-9.4', { + 'checksums': ['d9d3665c5f3d49f698fb4675daf40a0550601e86db3dc00f296413ceb1099ced'], }), - ('GGally', '1.4.0', { - 'checksums': ['9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe'], + ('GGally', '1.5.0', { + 'checksums': ['069261cd469e2d2c8c794b2956e69c356b471eccfc45a60c55e55dfd83185a20'], }), ('beanplot', '1.2', { 'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'], @@ -1280,8 +1279,8 @@ exts_list = [ ('BiasedUrn', '1.07', { 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], }), - ('TeachingDemos', '2.10', { - 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], + ('TeachingDemos', '2.12', { + 'checksums': ['3e75405ce1affa406d6df85e06f96381412bc7a2810b25d8c81bfe64c4698644'], }), ('kohonen', '3.0.10', { 'checksums': ['996956ea46a827c9f214e4f940a19304a0ff35bda707d4d7312f80d3479067b2'], @@ -1331,8 +1330,8 @@ exts_list = [ ('uroot', '2.1-0', { 'checksums': ['3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2'], }), - ('forecast', '8.11', { - 'checksums': ['a12718b7ac1ab78708ef244e4a1cfd044af128de590e14b1d8aab3342d6cd12b'], + ('forecast', '8.12', { + 'checksums': ['eb607fd584d66abf39b14c00d50111304e892a6e0778c9a8354195c6c92f92f9'], }), ('fma', '2.4', { 'checksums': ['69a94c3bd464176a80232d49fcd04d478d4dd59f9bf128d6a9f46e49612d27f4'], @@ -1364,8 +1363,8 @@ exts_list = [ ('pracma', '2.2.9', { 'checksums': ['0cea0ff5e88643df121e07b9aebfe57084c61e11801680039752f371fe87bf1e'], }), - ('RCurl', '1.98-1.1', { - 'checksums': ['6eca9172be1b32786950290eddb626caa5d6b0e8351ff458dd06ecd2215711ff'], + ('RCurl', '1.98-1.2', { + 'checksums': ['5d74a0cdc3c5684b0348b959f67039e3c2a5da2bbb6176f6800a94124895a7a8'], }), ('bio3d', '2.4-1', { 'checksums': ['679fbd87fe9fb82a65427d281d3b68906509e411270cd87d2deb95d404333c1f'], @@ -1397,8 +1396,8 @@ exts_list = [ ('dimRed', '0.2.3', { 'checksums': ['e6e56e3f6999ebdc326e64ead5269f3aaf61dd587beefafb7536ac3890370d84'], }), - ('lubridate', '1.7.4', { - 'checksums': ['510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891'], + ('lubridate', '1.7.8', { + 'checksums': ['3da19922fc373e113ecc58c4984955ba26da703edc9c991bd444b7077d4b553c'], }), ('ddalpha', '1.3.11', { 'checksums': ['c30b4a3a9549cb4dc0a8e51e06f5b6e4c457c5326acc8f4680968c920f59b6e9'], @@ -1412,23 +1411,23 @@ exts_list = [ ('recipes', '0.1.10', { 'checksums': ['4f345e31568e41b3efb6c6333e8ccab032e293dbd0256299d922fe6c9532c985'], }), - ('caret', '6.0-85', { - 'checksums': ['da29d9bf30f519fd4ca7b7fc834f61d46fc99540e17d69afd065adcdbe70ab4b'], + ('caret', '6.0-86', { + 'checksums': ['da4a1c7c3fbf645c5b02871e563a77404622b83623f0d1c5dc1425de7aa4ce37'], }), ('adabag', '4.2', { 'checksums': ['47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81'], }), - ('parallelMap', '1.4', { - 'checksums': ['fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b'], + ('parallelMap', '1.5.0', { + 'checksums': ['4afa727f4786279718cc799e45e91859a46f5cbc1ee652b0f47ae3b9f9d45e4e'], }), - ('ParamHelpers', '1.13', { - 'checksums': ['b9b5212a485f441504716fcddf4fd7376bf3b909aae049c7394245e853424e79'], + ('ParamHelpers', '1.14', { + 'checksums': ['b17652d0a69de3241a69f20be4ad1bfe02c413328a17f3c1ac7b73886a6ba2eb'], }), ('ggvis', '0.4.5', { 'checksums': ['82373c3565c299279f6849f798cc39127b2b3f7ff2deee1946528474824b3124'], }), - ('mlr', '2.17.0', { - 'checksums': ['ce8bb1c890821b951cb84a50697fc11e39d5fe79198f00380ceea207f77bf274'], + ('mlr', '2.17.1', { + 'checksums': ['0b71b9d00c627647cf5fc1f456d4445f025c90be2f974e05ccdb84e25ba1923b'], }), ('unbalanced', '2.0', { 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], @@ -1442,8 +1441,8 @@ exts_list = [ ('abc', '2.1', { 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), - ('lhs', '1.0.1', { - 'checksums': ['a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53'], + ('lhs', '1.0.2', { + 'checksums': ['e2945192740fb088b210786006b311d3d4e7da967733a1998380d597320c1158'], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], @@ -1478,8 +1477,8 @@ exts_list = [ ('remotes', '2.1.1', { 'checksums': ['4e590746fce618094089372b185e1ea234b3337b23c44c44118e942d0fb5118b'], }), - ('fs', '1.3.2', { - 'checksums': ['5ff565c2825ea68f0d55fd7f2ffebe58997df471cb24db8633ea34d2a95b60f0'], + ('fs', '1.4.1', { + 'checksums': ['ae9103dff26ca56a34901408bd650a2949f491b2a0886c686a51a179d38b7a4e'], }), ('clisymbols', '1.2.0', { 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], @@ -1490,20 +1489,20 @@ exts_list = [ ('gh', '1.1.0', { 'checksums': ['de9faf383c3fe5e87a75391d82cf71b1331b3c80cd00c4203146a303825d89ad'], }), - ('usethis', '1.5.1', { - 'checksums': ['9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d'], + ('usethis', '1.6.1', { + 'checksums': ['60339059a97ed07dea7f8908b828b5bb42e0fd0b471165c061bc9660b0d59d6f'], }), - ('DT', '0.12', { - 'checksums': ['239906a884a485fd09e50bf10a52268f62ffd4ba9569499c4d92055511120901'], + ('DT', '0.13', { + 'checksums': ['79a073fe96980ce150d790ab76133c9e80bd463270c34d149c03934a622d63b5'], }), - ('rex', '1.1.2', { - 'checksums': ['bd3c74ceaf335336f5dd04314d0a791f6311e421a2158f321f5aab275f539a2a'], + ('rex', '1.2.0', { + 'checksums': ['06b491f1469078862e40543fd74e1d38b2e0fb61fdf01c8083add4b11ac2eb54'], }), ('covr', '3.5.0', { 'checksums': ['cb919912018130164a40803ac573a37dde2186678c058c03c6303d79604979df'], }), - ('devtools', '2.2.2', { - 'checksums': ['e988f435fbb5cfc89c4a4755a999dd08f176dd63151dc340e3bf5d1a91140bae'], + ('devtools', '2.3.0', { + 'checksums': ['4fc375c171335c67bd71df4e0b1b3dff2ae3aa17b3e0566b790ba0808b39dcd0'], }), ('Rook', '1.1-1', { 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], @@ -1517,8 +1516,8 @@ exts_list = [ ('Lmoments', '1.3-1', { 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], }), - ('distillery', '1.0-6', { - 'checksums': ['4910e2952f767c1062d7cbe648c90a97009e2b3da316c6b33f6d022cd38b23d6'], + ('distillery', '1.0-7', { + 'checksums': ['898833ceceed5291b4a02bf62c6fa5b78dd7837f9cc5a42b87a08672c7dae270'], }), ('extRemes', '2.0-11', { 'checksums': ['75fbdeef677c81cf5661b8df3df4090c55f53e9bb96bb138b498eb0fbbf5af42'], @@ -1571,8 +1570,8 @@ exts_list = [ ('matrixcalc', '1.0-3', { 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], }), - ('arm', '1.10-1', { - 'checksums': ['6f1158c9295e65bd649139224497d3356189b931ff143f9b374daae72548776f'], + ('arm', '1.11-1', { + 'checksums': ['7b82dbe8c5141546d11b0af656a6addda4c07f06fc165d01c7c1e39540b55444'], }), ('mi', '1.0', { 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], @@ -1610,8 +1609,8 @@ exts_list = [ ('glasso', '1.11', { 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], }), - ('huge', '1.3.4', { - 'checksums': ['23165f49ec9e67ca3506cc83abbbf8eb3f38c5e19c092133189b7ca17690c31e'], + ('huge', '1.3.4.1', { + 'checksums': ['78ef9eae464d52c5247998b9514a81b178419b857b1a6c00d885e3ae6c03a886'], }), ('d3Network', '0.5.2.1', { 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], @@ -1622,8 +1621,8 @@ exts_list = [ ('pbapply', '1.4-2', { 'checksums': ['ac19f209f36f4fa3d0f5b14b6cc5b0c279996fb9d3e86c848c0f6d03c025b3f6'], }), - ('graphlayouts', '0.6.0', { - 'checksums': ['8097d34cd4ae86fd2b806970513869c62305d54cdd878be64fe7ce33aa0940d1'], + ('graphlayouts', '0.7.0', { + 'checksums': ['20464b60376d9f8d522eec6a7495054b1715e4919f10e9a049868d8866398c9e'], }), ('tweenr', '1.0.1', { 'checksums': ['efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b'], @@ -1661,8 +1660,8 @@ exts_list = [ ('minpack.lm', '1.2-1', { 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], }), - ('rootSolve', '1.8.2', { - 'checksums': ['94140ba375480fadae3fb7334000e1d62977b93e70bf0d963efffdcc3e614766'], + ('rootSolve', '1.8.2.1', { + 'checksums': ['488451182663197ae4513e46e24f72cadb2297d35a58a3007a0dbf1bf0833031'], }), ('diagram', '1.6.4', { 'checksums': ['7c2bc5d5d634c3b8ca7fea79fb463e412962d88f47a77a74c811cc62f375ce38'], @@ -1730,8 +1729,8 @@ exts_list = [ ('tsne', '0.1-3', { 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], }), - ('sn', '1.5-5', { - 'checksums': ['2e913f4ef22bbaf19e5fe4588ec8643d8f5f008c51d2cf4358e285d800f3be7a'], + ('sn', '1.6-1', { + 'checksums': ['80071625131256147f94a1a35b6f0cabd6de8b225f16860e398b6a8ca688d96a'], }), ('tclust', '1.4-1', { 'checksums': ['4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e'], @@ -1754,8 +1753,8 @@ exts_list = [ ('VIM', '5.1.1', { 'checksums': ['ca1430103b6bd658e318bbbbd9c25763d11d0b3f52706b1a7ea7fafd408e4270'], }), - ('proxy', '0.4-23', { - 'checksums': ['9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d'], + ('proxy', '0.4-24', { + 'checksums': ['8cff9bf036475941a7c44ba9bb5e2f6d4777d49ab3daaeb52d23f4b2af6d9c7c'], }), ('smoother', '1.1', { 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], @@ -1784,8 +1783,8 @@ exts_list = [ ('bst', '0.3-17', { 'checksums': ['1ed161d33a7304abfa2fb23daeda2f870ad8483b7fa9b91e6fc8ced21fd8f074'], }), - ('mpath', '0.3-23', { - 'checksums': ['197f9e8b8c4c1ee6401fa15048ce47d4e0180bd78170a95896a3c77f741a110a'], + ('mpath', '0.3-25', { + 'checksums': ['3332f74255520152cb2149bdff24ad650a036161a7629f686c8fee804c0336e8'], }), ('timereg', '1.9.4', { 'checksums': ['fbf4eeee1648fceb98773156764c32b3a9481f0fb9f8dc3a9d0331a9051cb54b'], @@ -1814,8 +1813,8 @@ exts_list = [ ('limSolve', '1.5.6', { 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], }), - ('dbplyr', '1.4.2', { - 'checksums': ['b783f0da2c09a1e63f41168b02c0715b08820f02a351f7ab0aaa688432754de0'], + ('dbplyr', '1.4.3', { + 'checksums': ['69ac7b4022c691e3822fc73fabb3bf073405d5a433c52f5f0f98cf90a1d228ea'], }), ('modelr', '0.1.6', { 'checksums': ['d7e5f3ddf0b3e6520ca06229471f5bcd9e371e2fecd53c03202b474c2a1955f4'], @@ -1847,8 +1846,8 @@ exts_list = [ ('globals', '0.12.5', { 'checksums': ['1519a7668b4b549c081f60a5f6b71d8d1dc8833f618125f6c0e4caf8b48a48c1'], }), - ('future', '1.16.0', { - 'checksums': ['b50db0f28712c70b4c6a670d1c86b218e20870cc13b03ac45dc5d929168058f5'], + ('future', '1.17.0', { + 'checksums': ['2fa3b88439eaa33901669295186d04eb54f033257015683cf8a2e3c7f83b9e34'], }), ('gdistance', '1.3-1', { 'checksums': ['0e9a7ab4fb75c2990ff7b85aa0661aaadbf4804f2a92fac9dd6d3c75db346813'], @@ -1883,11 +1882,11 @@ exts_list = [ ('gmp', '0.5-13.6', { 'checksums': ['39a61618cc9eeabd00665cc5f24721e75f0dec8268059a0d18c907c2adf85a48'], }), - ('spaMM', '3.1.27', { - 'checksums': ['36db1da0b5f12f60f665339b400c0008a4b2205a0735af9b654addd8e9b404a9'], + ('spaMM', '3.2.0', { + 'checksums': ['40d54ad52c4839f33baa1e488e1e76042e57083ff7780f9c5640c49340ff2999'], }), - ('DHARMa', '0.2.7', { - 'checksums': ['35100fed263607c9a31c1ea87a429995e92202a7d61a4b8f5692d3f3cb36fa8d'], + ('DHARMa', '0.3.0', { + 'checksums': ['1c7ac2f1897ca62e0ebb7367c4b31866515c8503d0fa645fa5e8ac5172310298'], }), ('mvnfast', '0.2.5', { 'checksums': ['21b9fa72d1e3843513908aaacd6c4d876cc7a9339782d0151b24910df2975f88'], @@ -2006,13 +2005,13 @@ exts_list = [ ('rappdirs', '0.3.1', { 'checksums': ['2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a'], }), - ('reticulate', '1.14', { - 'checksums': ['76be64acf30d5ecba225794a818715dc83090ac92df8b3a52da7d39fe84f8b45'], + ('reticulate', '1.15', { + 'checksums': ['47db3e9c9424263ade15287da8e74f6ba261a936b644b197dba6772853b7b50d'], }), - ('hdf5r', '1.3.1', { + ('hdf5r', '1.3.2', { 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'preinstallopts': "unset LIBS && ", - 'checksums': ['fd66dda7e65ad6a7baaa362faa11b2545cca3a8cba5aaeeeebf49bed37137143'], + 'checksums': ['31493d9dde9705543e5474c937fa5b4b64895ae1dd6ee51d7039dd95a6015730'], }), ('DTRreg', '1.5', { 'checksums': ['eb9b4d98b25eec304a447db302f618a75180f8d8fe0f5728ecd7e85957613456'], @@ -2026,14 +2025,14 @@ exts_list = [ ('energy', '1.7-7', { 'checksums': ['67b88fb33ee6e7bec2e4fe356a4efd36f70c3cf9b0ebe2f6d9da9ec96de9968f'], }), - ('compositions', '1.40-4', { - 'checksums': ['2a99cead22cc2e0708f4be19bb12bada9b39fdcdffefc014408c0d193da5807c'], + ('compositions', '1.40-5', { + 'checksums': ['879e296037b0b3c52cfe48556820500b94d4eea16ec2b40f85988b65c5f72a51'], }), ('clustree', '0.4.2', { 'checksums': ['5d6b8ee3cbbcdd235a7abe4107429e45847ed09ec1cdb572ad6efb9d88dff82e'], }), - ('plotly', '4.9.2', { - 'checksums': ['a5d275ed8400bf9ebe38c075ce1cc4511992e38cbe235537ed0d3f072d1efca7'], + ('plotly', '4.9.2.1', { + 'checksums': ['f45eae325ab7e7924b0be098bad866ce003d657cf63e137104401c2dd4401db8'], }), ('tweedie', '2.3.2', { 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], @@ -2083,8 +2082,8 @@ exts_list = [ ('dtangle', '2.0.9', { 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], }), - ('mcmc', '0.9-6.1', { - 'checksums': ['692bb1cd4a9d09ddcbec3bcaaa4daccd06303f12188dfe51a95b467f558336c4'], + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], }), ('MCMCpack', '1.4-6', { 'checksums': ['6bcd018d6fa589a6854ee1bcea18b9d6c4095f3deae9058f69afbb09cba873c7'], @@ -2110,8 +2109,8 @@ exts_list = [ ('mltools', '0.3.5', { 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], }), - ('h2o', '3.28.0.4', { - 'checksums': ['580dc6115b9ac21352eab2f94fa88eca2b7480a5886f0c3c18f247be1ce14bdb'], + ('h2o', '3.30.0.1', { + 'checksums': ['cb11ef58a7d7dfd3a9193686ddd9c8a9f988b33a69656d8b3e8f59082068b0f5'], }), ('mlegp', '3.1.7', { 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], @@ -2140,8 +2139,8 @@ exts_list = [ ('GenSA', '1.1.7', { 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], }), - ('rematch2', '2.1.0', { - 'checksums': ['78677071bd44b40e562df1da6f0c6bdeae44caf973f97ff8286b8c994db59f01'], + ('rematch2', '2.1.1', { + 'checksums': ['d0423a418e8b46ac3a4819af7a7d19c39ca7c8c862c1e9a1c1294aa19152518f'], }), ('parsedate', '1.2.0', { 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], @@ -2191,8 +2190,8 @@ exts_list = [ ('BMA', '3.18.12', { 'checksums': ['cbabb77d92b09a11a986ad03950322e78dff743f82ff67fda51d32e44135dd79'], }), - ('BCEE', '1.2', { - 'checksums': ['0b1183458d625ef5dd0962fc77ca1326e77754a2c04be11fb002057abcb65a22'], + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], }), ('bacr', '1.0.1', { 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], @@ -2240,8 +2239,8 @@ exts_list = [ ('abe', '3.0.1', { 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], }), - ('SignifReg', '2.1', { - 'checksums': ['d21959ce5b1ee20efd1483f6020b57e5f6616bd525af77a7bd325501cc670606'], + ('SignifReg', '3.0', { + 'checksums': ['ada4e1f8cbb08ba8ff16275ec5f9a453857e0cab63b70d42753989ab4c716b7b'], }), ('bbmle', '1.0.23.1', { 'checksums': ['60421eb01190b741ab14885eaf1088f51d49dcf70e58c42b360489bca04e745c'], @@ -2261,14 +2260,14 @@ exts_list = [ ('ISOcodes', '2020.03.16', { 'checksums': ['160eb4ea23be53305e4e728002c8f5d3852d89155f538deccb734e7c8ad4e1c3'], }), - ('stopwords', '1.0', { - 'checksums': ['9b727a5d827ac8dcfa6329140d294dcf964a06d80132b4ca434330d0ee02b1da'], + ('stopwords', '2.0', { + 'checksums': ['5cca60ce9f44406486e0dca2e36cec2488096c3558b45fc3bd0e7b6d1500af94'], }), ('janeaustenr', '0.1.5', { 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], }), - ('SnowballC', '0.6.0', { - 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], }), ('tokenizers', '0.2.1', { 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], @@ -2276,11 +2275,11 @@ exts_list = [ ('hunspell', '3.0', { 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], }), - ('topicmodels', '0.2-9', { - 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], + ('topicmodels', '0.2-11', { + 'checksums': ['9c26b4d967be6ec26834a39f04aa92b059ea9503eb70c700e1c0a7a43637b74a'], }), - ('tidytext', '0.2.3', { - 'checksums': ['c103f98f5cbbb5a4ea4c893520ea5eb38b9c5097e5325d7efd4f7e3afe71068b'], + ('tidytext', '0.2.4', { + 'checksums': ['46ff59063b6a519c9eb606ae135ef31d7073ac729e4a912c9f77e234801b933d'], }), ('splitstackshape', '1.4.8', { 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], @@ -2303,8 +2302,8 @@ exts_list = [ ('HiddenMarkov', '1.8-11', { 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], }), - ('lmerTest', '3.1-1', { - 'checksums': ['520ef83e9a7c58e3c5b7175fbda902b747b2e01c24b53714ede81a6a87de5b64'], + ('lmerTest', '3.1-2', { + 'checksums': ['385870873fd303c2caa4ac43e2df0ca5aa36ddb484bfb4eefbc5c4ac4bef6de2'], }), ('loo', '2.2.0', { 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'], From 0aa9aaaa93d0335846b0a340f9f7d1677dfd9e55 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 29 Apr 2020 12:58:16 +0200 Subject: [PATCH 279/431] use https in HDF-EOS-2.20-GCCcore-7.3.0.eb --- easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb index 34d17fa122e..f75fec3c148 100644 --- a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF-EOS' version = '2.20' -homepage = 'http://hdfeos.org/' +homepage = 'https://hdfeos.org/' description = """HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath.""" @@ -23,7 +23,7 @@ builddependencies = [ ('binutils', '2.30'), ] -dependencies = [ +dependencies = [ ('HDF', '4.2.14'), ('Szip', '2.1.1'), ] From bb97efc4885e38b800fe10e65f4843949bca52c0 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 29 Apr 2020 12:58:43 +0200 Subject: [PATCH 280/431] adding easyconfigs: HDF-EOS5-1.16-foss-2018b.eb --- .../h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb new file mode 100644 index 00000000000..63ab642efd2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS5' +version = '1.16' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/latest_release/', + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/previous_releases/', +] + +sources = ['%(name)s.%(version)s.tar.Z'] + +checksums = ['7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452'] + +dependencies = [ + ('HDF5', '1.10.2'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF5/bin/h5pcc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HE5_HdfEosDef.h', 'include/HE5_GctpFunc.h', 'lib/libGctp.la', 'lib/libhe5_hdfeos.la'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From 7fdb9106167c3e1cb806e85c365601d28f076386 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 29 Apr 2020 13:01:36 +0200 Subject: [PATCH 281/431] replace PCRE for PCRE2 in R-4.0.0-foss-2020a.eb --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index daac80e76be..d1b1100bfc1 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -25,7 +25,7 @@ dependencies = [ ('XZ', '5.2.5'), ('zlib', '1.2.11'), ('SQLite', '3.31.1'), - ('PCRE', '8.44'), + ('PCRE2', '10.34'), ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), From 3dcae476e7fe4c0a0f2a8d365e4e4f45ffd2262c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 14:13:59 +0200 Subject: [PATCH 282/431] add patch for liquidSVM extension to R 4.0.0 easyconfig to fix installation on POWER --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index d1b1100bfc1..1d5441ece39 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2102,6 +2102,13 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'checksums': ['15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'], + 'patches': ['liquidSVM-1.2.4-fix_ppc_build.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', + '21e65c8ff3f14678e43c19b4f8c36fce9bed796965abf161a147040941fc55ab', # liquidSVM-1.2.4-fix_ppc_build.patch + ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], From 23f3e348a992dd7de3797bb2fa52bd30754e1079 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 14:56:40 +0200 Subject: [PATCH 283/431] {*}[*/2020a] VTK v8.2.0, LAMMPS 3Mar2020, PLUMED v2.6.0, GDAL v3.0.4 + more w/ Python 3.8.2 --- .../GDAL-3.0.4-foss-2020a-Python-3.8.2.eb | 61 + .../GDAL-3.0.4-intel-2020a-Python-3.8.2.eb | 63 + ...-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb | 33 + .../g/GSL/GSL-2.6-iccifort-2020.1.217.eb | 25 + .../h5py-2.10.0-foss-2020a-Python-3.8.2.eb | 37 + .../h5py-2.10.0-intel-2020a-Python-3.8.2.eb | 37 + .../k/kim-api/kim-api-2.1.3-foss-2020a.eb | 44 + .../k/kim-api/kim-api-2.1.3-intel-2020a.eb | 44 + ...3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb | 93 + ...mps-stable_3Mar2020_hack_openmp_gcc9.patch | 3969 +++++++++++++++++ .../molmod-1.4.5-foss-2020a-Python-3.8.2.eb | 37 + .../molmod-1.4.5-intel-2020a-Python-3.8.2.eb | 40 + .../molmod-1.4.5_deprecated_time_method.patch | 42 + .../networkx-2.4-foss-2020a-Python-3.8.2.eb | 26 + .../PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb | 60 + .../PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb | 60 + .../s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb | 42 + .../s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb | 42 + ...it-build-0.10.0-foss-2020a-Python-3.8.2.eb | 27 + .../VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb | 97 + .../VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb | 97 + .../VTK-8.2.0_python_3.8_compatibility.patch | 176 + .../yaff-1.6.0-foss-2020a-Python-3.8.2.eb | 47 + .../yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 47 + 24 files changed, 5246 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb create mode 100644 easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..f60ac42d5a0 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277', # gdal-3.0.4.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.8.1', versionsuffix), + ('SQLite', '3.31.1'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.69.1'), + ('PCRE', '8.44'), + ('PROJ', '7.0.0'), + ('libgeotiff', '1.5.1'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..7cd0e55a80d --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277', # gdal-3.0.4.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.8.1', versionsuffix), + ('SQLite', '3.31.1'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.69.1'), + ('PCRE', '8.44'), + ('PROJ', '7.0.0'), + ('libgeotiff', '1.5.1'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +prebuildopts = 'export LDSHARED="$CC -shared" && ' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb new file mode 100644 index 00000000000..0bf4e9a4ce9 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-3.7.2_fix-Python3.patch'] +checksums = [ + '4258af4308deb9dbb5047379026b4cd9838513627cb943a44e16c40e42ae17f7', # geos-3.8.1.tar.bz2 + 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch +] + +dependencies = [('Python', '3.8.2')] + +builddependencies = [('SWIG', '4.0.1')] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb new file mode 100644 index 00000000000..af6a5a7298c --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..010d200891a --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] + +builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +use_pip = False +download_dep_fail = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) +options = {'modulename': False} +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..71353b9b531 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] + +builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +use_pip = False +download_dep_fail = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) +options = {'modulename': False} +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb new file mode 100644 index 00000000000..3fc9c6cb46f --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.1.3' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['88a5416006c65a2940d82fad49de0885aead05bfa8b59f87d287db5516b9c467'] + +dependencies = [ + ('CMake', '3.16.4'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True +build_type = 'Release' + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb new file mode 100644 index 00000000000..944a2f80e09 --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.1.3' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['88a5416006c65a2940d82fad49de0885aead05bfa8b59f87d287db5516b9c467'] + +dependencies = [ + ('CMake', '3.16.4'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True +build_type = 'Release' + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb new file mode 100644 index 00000000000..589ce20cd25 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb @@ -0,0 +1,93 @@ +name = 'LAMMPS' +version = '3Mar2020' +local_python_versionsuffix = '-Python-%(pyver)s' +versionsuffix = local_python_versionsuffix +versionsuffix += '-kokkos' + +homepage = 'https://lammps.sandia.gov/' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s.tar.gz'] +# See https://github.com/lammps/lammps/pull/1483 for why this is needed +patches = ['lammps-stable_3Mar2020_hack_openmp_gcc9.patch'] +checksums = [ + 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz + '41a0bcb828be22d38bb489bbd4b1fd7803d7771a2308371f01e961c52b8c869f', # lammps-stable_3Mar2020_hack_openmp_gcc9.patch +] + +local_source_dir_name = '%(namelower)s-%(version)s' + +builddependencies = [ + ('CMake', '3.16.4'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.0', local_python_versionsuffix), +] + +dependencies = [ + ('Python', '3.8.2'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('netCDF', '4.7.4'), + ('GSL', '2.6'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.69.1'), + ('HDF5', '1.10.6'), + ('tbb', '2020.1'), + ('PCRE', '8.44'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.2.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.1.3'), + ('Eigen', '3.3.7'), + ('yaff', '1.6.0', local_python_versionsuffix), + ('PLUMED', '2.6.0', local_python_versionsuffix), + ('ScaFaCoS', '1.0.1'), + ('VTK', '8.2.0', local_python_versionsuffix), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options +# configopts = " " + +# auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# +# not enabled (yet), needs more work/additional dependencies: +# 'LATTE', - https://lammps.sandia.gov/doc/Build_extras.html#latte-package +# 'MSCG', - https://lammps.sandia.gov/doc/Build_extras.html#mscg-package +general_packages = [ + 'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE', + 'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC', + 'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID', + 'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI', +] + +# not enabled (yet), needs more work/additional dependencies: +# ADIOS - https://lammps.sandia.gov/doc/Build_extras.html#user-adios-package +# AWPMD - https://lammps.sandia.gov/doc/Build_extras.html#user-awpmd-package +# QUIP - https://lammps.sandia.gov/doc/Build_extras.html#user-quip-package +user_packages = [ + 'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE', + 'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC', + 'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC', + 'SCAFACOS', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', 'VTK' +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch new file mode 100644 index 00000000000..f36d414562c --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_hack_openmp_gcc9.patch @@ -0,0 +1,3969 @@ +Patch generated by recursively applying +lammps-stable_3Mar2020.orig/src/USER-OMP/hack_openmp_for_pgi_gcc9.sh +to the 'src' directory, which allows this version of LAMMPS to build +for GCC 9. + +Alan O'Cais 20200324 +diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_atom_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_atom_mpiio.cpp +--- lammps-stable_3Mar2020.orig/src/MPIIO/dump_atom_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/MPIIO/dump_atom_mpiio.cpp 2020-03-20 16:49:44.619401713 +0100 +@@ -587,7 +587,7 @@ + mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); + mpifh_buffer_line_per_thread[i][0] = '\0'; + +-#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) ++#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) + { + int tid = omp_get_thread_num(); + int m=0; +@@ -677,7 +677,7 @@ + mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); + mpifh_buffer_line_per_thread[i][0] = '\0'; + +-#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) ++#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) + { + int tid = omp_get_thread_num(); + int m=0; +diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_cfg_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_cfg_mpiio.cpp +--- lammps-stable_3Mar2020.orig/src/MPIIO/dump_cfg_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/MPIIO/dump_cfg_mpiio.cpp 2020-03-20 16:49:44.623401733 +0100 +@@ -365,7 +365,7 @@ + mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); + mpifh_buffer_line_per_thread[i][0] = '\0'; + +-#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) ++#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) + { + int tid = omp_get_thread_num(); + int m=0; +diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_custom_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_custom_mpiio.cpp +--- lammps-stable_3Mar2020.orig/src/MPIIO/dump_custom_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/MPIIO/dump_custom_mpiio.cpp 2020-03-20 16:49:44.627401752 +0100 +@@ -612,7 +612,7 @@ + mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); + mpifh_buffer_line_per_thread[i][0] = '\0'; + +-#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) ++#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) + { + int tid = omp_get_thread_num(); + int m=0; +diff -Nru lammps-stable_3Mar2020.orig/src/MPIIO/dump_xyz_mpiio.cpp lammps-stable_3Mar2020/src/MPIIO/dump_xyz_mpiio.cpp +--- lammps-stable_3Mar2020.orig/src/MPIIO/dump_xyz_mpiio.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/MPIIO/dump_xyz_mpiio.cpp 2020-03-20 16:49:44.631401773 +0100 +@@ -350,7 +350,7 @@ + mpifh_buffer_line_per_thread[i] = (char *) malloc(DUMP_BUF_CHUNK_SIZE * sizeof(char)); + mpifh_buffer_line_per_thread[i][0] = '\0'; + +-#pragma omp parallel default(none) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) ++#pragma omp parallel default(shared) shared(bufOffset, bufRange, bufLength, mpifhStringCountPerThread, mpifh_buffer_line_per_thread, mybuf) + { + int tid = omp_get_thread_num(); + int m=0; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_saed.cpp lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_saed.cpp +--- lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_saed.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_saed.cpp 2020-03-20 16:49:45.761407407 +0100 +@@ -418,7 +418,7 @@ + double frac = 0.1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(offset,ASFSAED,typelocal,xlocal,Fvec,m,frac) ++#pragma omp parallel default(shared) shared(offset,ASFSAED,typelocal,xlocal,Fvec,m,frac) + #endif + { + double *f = new double[ntypes]; // atomic structure factor by type +diff -Nru lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_xrd.cpp lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_xrd.cpp +--- lammps-stable_3Mar2020.orig/src/USER-DIFFRACTION/compute_xrd.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-DIFFRACTION/compute_xrd.cpp 2020-03-20 16:49:45.765407427 +0100 +@@ -353,7 +353,7 @@ + double frac = 0.1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(typelocal,xlocal,Fvec,m,frac,ASFXRD) ++#pragma omp parallel default(shared) shared(typelocal,xlocal,Fvec,m,frac,ASFXRD) + #endif + { + double *f = new double[ntypes]; // atomic structure factor by type +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_charmm_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/angle_charmm_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_charmm_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/angle_charmm_intel.cpp 2020-03-20 16:49:46.332410255 +0100 +@@ -134,7 +134,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oeangle,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/angle_harmonic_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/angle_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/angle_harmonic_intel.cpp 2020-03-20 16:49:46.336410275 +0100 +@@ -134,7 +134,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oeangle,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_fene_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/bond_fene_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_fene_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/bond_fene_intel.cpp 2020-03-20 16:49:46.339410290 +0100 +@@ -127,7 +127,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oebond,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/bond_harmonic_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/bond_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/bond_harmonic_intel.cpp 2020-03-20 16:49:46.342410305 +0100 +@@ -127,7 +127,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oebond,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_charmm_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_charmm_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_charmm_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_charmm_intel.cpp 2020-03-20 16:49:46.347410330 +0100 +@@ -148,7 +148,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oevdwl,oecoul,oedihedral,ov0,ov1,ov2,ov3,ov4,ov5, \ + opv0,opv1,opv2,opv3,opv4,opv5) +@@ -522,7 +522,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oevdwl,oecoul,oedihedral,ov0,ov1,ov2,ov3,ov4,ov5, \ + opv0,opv1,opv2,opv3,opv4,opv5) +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_fourier_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_fourier_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_fourier_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_fourier_intel.cpp 2020-03-20 16:49:46.351410350 +0100 +@@ -127,7 +127,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_harmonic_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_harmonic_intel.cpp 2020-03-20 16:49:46.354410364 +0100 +@@ -127,7 +127,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_opls_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/dihedral_opls_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/dihedral_opls_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/dihedral_opls_intel.cpp 2020-03-20 16:49:46.358410384 +0100 +@@ -131,7 +131,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oedihedral,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/fix_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/fix_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/fix_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/fix_intel.cpp 2020-03-20 16:49:46.364410414 +0100 +@@ -220,7 +220,7 @@ + comm->nthreads = nomp; + } else { + int nthreads; +- #pragma omp parallel default(none) shared(nthreads) ++ #pragma omp parallel default(shared) + nthreads = omp_get_num_threads(); + comm->nthreads = nthreads; + } +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_cvff_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/improper_cvff_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_cvff_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/improper_cvff_intel.cpp 2020-03-20 16:49:46.385410519 +0100 +@@ -138,7 +138,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oeimproper,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_harmonic_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/improper_harmonic_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/improper_harmonic_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/improper_harmonic_intel.cpp 2020-03-20 16:49:46.389410539 +0100 +@@ -139,7 +139,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(f_start,f_stride,fc) \ + reduction(+:oeimproper,ov0,ov1,ov2,ov3,ov4,ov5) + #endif +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/npair_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/npair_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/npair_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/npair_intel.cpp 2020-03-20 16:49:46.414410664 +0100 +@@ -263,7 +263,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(overflow, nstencilp, binstart, binend) + #endif + { +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_disp_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/pppm_disp_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_disp_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/pppm_disp_intel.cpp 2020-03-20 16:49:46.509411137 +0100 +@@ -728,7 +728,7 @@ + int flag = 0; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr, delx, dely, delz, sft, p2g, nup, nlow, nxlo,\ + nylo, nzlo, nxhi, nyhi, nzhi) reduction(+:flag) if(!_use_lrt) + #endif +@@ -802,7 +802,7 @@ + int nthr = comm->nthreads; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, nlocal, global_density) if(!_use_lrt) + #endif + { +@@ -908,7 +908,7 @@ + + // reduce all the perthread_densities into global_density + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, global_density) if(!_use_lrt) + #endif + { +@@ -950,7 +950,7 @@ + int nthr = comm->nthreads; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, nlocal, global_density) if(!_use_lrt) + #endif + { +@@ -1058,7 +1058,7 @@ + + // reduce all the perthread_densities into global_density + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, global_density) if(!_use_lrt) + #endif + { +@@ -1233,7 +1233,7 @@ + int nthr = comm->nthreads; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, nlocal, global_density) if(!_use_lrt) + #endif + { +@@ -1342,7 +1342,7 @@ + + // reduce all the perthread_densities into global_density + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, global_density) if(!_use_lrt) + #endif + { +@@ -1385,7 +1385,7 @@ + + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -1535,7 +1535,7 @@ + FFT_SCALAR * _noalias const particle_ekz = this->particle_ekz; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -1733,7 +1733,7 @@ + + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -1880,7 +1880,7 @@ + FFT_SCALAR * _noalias const particle_ekz = this->particle_ekz; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -2077,7 +2077,7 @@ + + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -2311,7 +2311,7 @@ + FFT_SCALAR * _noalias const particle_ekz6 = this->particle_ekz6; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -2602,7 +2602,7 @@ + + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -2761,7 +2761,7 @@ + int nthr = comm->nthreads; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +diff -Nru lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_intel.cpp lammps-stable_3Mar2020/src/USER-INTEL/pppm_intel.cpp +--- lammps-stable_3Mar2020.orig/src/USER-INTEL/pppm_intel.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-INTEL/pppm_intel.cpp 2020-03-20 16:49:46.515411167 +0100 +@@ -360,7 +360,7 @@ + error->one(FLERR,"Non-numeric box dimensions - simulation unstable"); + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) reduction(+:flag) if(!_use_lrt) + #endif + { +@@ -434,7 +434,7 @@ + nthr = comm->nthreads; + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, nlocal, global_density) if(!_use_lrt) + #endif + { +@@ -537,7 +537,7 @@ + // reduce all the perthread_densities into global_density + if (nthr > 1) { + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nthr, global_density) if(!_use_lrt) + #endif + { +@@ -586,7 +586,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +@@ -737,7 +737,7 @@ + } + + #if defined(_OPENMP) +- #pragma omp parallel default(none) \ ++ #pragma omp parallel default(shared) \ + shared(nlocal, nthr) if(!_use_lrt) + #endif + { +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_charmm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_charmm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_charmm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_charmm_omp.cpp 2020-03-20 16:49:48.136419251 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_class2_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_class2_omp.cpp 2020-03-20 16:49:48.139419266 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_delta_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_delta_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_delta_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_delta_omp.cpp 2020-03-20 16:49:48.141419276 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_omp.cpp 2020-03-20 16:49:48.144419291 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_periodic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_periodic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_periodic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_periodic_omp.cpp 2020-03-20 16:49:48.147419306 +0100 +@@ -49,7 +49,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_exp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_exp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_exp_omp.cpp 2020-03-20 16:49:48.149419316 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_shift_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_shift_omp.cpp 2020-03-20 16:49:48.152419330 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_squared_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_squared_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_cosine_squared_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_cosine_squared_omp.cpp 2020-03-20 16:49:48.154419341 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_dipole_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_dipole_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_dipole_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_dipole_omp.cpp 2020-03-20 16:49:48.157419355 +0100 +@@ -51,7 +51,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_omp.cpp 2020-03-20 16:49:48.160419370 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_simple_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_simple_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_fourier_simple_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_fourier_simple_omp.cpp 2020-03-20 16:49:48.164419390 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_harmonic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_harmonic_omp.cpp 2020-03-20 16:49:48.166419400 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_quartic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_quartic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_quartic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_quartic_omp.cpp 2020-03-20 16:49:48.169419415 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_sdk_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_sdk_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_sdk_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_sdk_omp.cpp 2020-03-20 16:49:48.171419425 +0100 +@@ -49,7 +49,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/angle_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/angle_table_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/angle_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/angle_table_omp.cpp 2020-03-20 16:49:48.174419440 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nanglelist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_class2_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_class2_omp.cpp 2020-03-20 16:49:48.177419455 +0100 +@@ -47,7 +47,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_expand_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_fene_expand_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_expand_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_fene_expand_omp.cpp 2020-03-20 16:49:48.179419465 +0100 +@@ -48,7 +48,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_fene_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_fene_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_fene_omp.cpp 2020-03-20 16:49:48.182419480 +0100 +@@ -48,7 +48,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_gromos_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_gromos_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_gromos_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_gromos_omp.cpp 2020-03-20 16:49:48.184419490 +0100 +@@ -44,7 +44,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_omp.cpp 2020-03-20 16:49:48.187419505 +0100 +@@ -46,7 +46,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp 2020-03-20 16:49:48.189419515 +0100 +@@ -46,7 +46,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_harmonic_shift_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_harmonic_shift_omp.cpp 2020-03-20 16:49:48.191419525 +0100 +@@ -46,7 +46,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_morse_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_morse_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_morse_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_morse_omp.cpp 2020-03-20 16:49:48.194419540 +0100 +@@ -46,7 +46,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_nonlinear_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_nonlinear_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_nonlinear_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_nonlinear_omp.cpp 2020-03-20 16:49:48.196419550 +0100 +@@ -46,7 +46,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_quartic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_quartic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_quartic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_quartic_omp.cpp 2020-03-20 16:49:48.199419565 +0100 +@@ -52,7 +52,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/bond_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/bond_table_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/bond_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/bond_table_omp.cpp 2020-03-20 16:49:48.202419580 +0100 +@@ -46,7 +46,7 @@ + const int inum = neighbor->nbondlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_charmm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_charmm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_charmm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_charmm_omp.cpp 2020-03-20 16:49:48.205419595 +0100 +@@ -56,7 +56,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_class2_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_class2_omp.cpp 2020-03-20 16:49:48.209419615 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp 2020-03-20 16:49:48.212419630 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_fourier_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_fourier_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_fourier_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_fourier_omp.cpp 2020-03-20 16:49:48.215419645 +0100 +@@ -49,7 +49,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_harmonic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_harmonic_omp.cpp 2020-03-20 16:49:48.218419660 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_helix_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_helix_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_helix_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_helix_omp.cpp 2020-03-20 16:49:48.222419680 +0100 +@@ -53,7 +53,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_multi_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_multi_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_multi_harmonic_omp.cpp 2020-03-20 16:49:48.227419705 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_nharmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_nharmonic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_nharmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_nharmonic_omp.cpp 2020-03-20 16:49:48.230419719 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_opls_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_opls_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_opls_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_opls_omp.cpp 2020-03-20 16:49:48.235419744 +0100 +@@ -51,7 +51,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_quadratic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_quadratic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_quadratic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_quadratic_omp.cpp 2020-03-20 16:49:48.238419759 +0100 +@@ -51,7 +51,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/dihedral_table_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/dihedral_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/dihedral_table_omp.cpp 2020-03-20 16:49:48.241419774 +0100 +@@ -113,7 +113,7 @@ + const int inum = neighbor->ndihedrallist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/domain_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/domain_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/domain_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/domain_omp.cpp 2020-03-20 16:49:48.244419789 +0100 +@@ -45,7 +45,7 @@ + const int nlocal = atom->nlocal; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + imageint idim,otherdims; +@@ -143,7 +143,7 @@ + const int num = n; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < num; i++) { + x[i].x = h[0]*x[i].x + h[5]*x[i].y + h[4]*x[i].z + boxlo[0]; +@@ -163,7 +163,7 @@ + const int num = n; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < num; i++) { + double delta0 = x[i].x - boxlo[0]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/ewald_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/ewald_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/ewald_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/ewald_omp.cpp 2020-03-20 16:49:48.247419804 +0100 +@@ -104,7 +104,7 @@ + v0=v1=v2=v3=v4=v5=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) reduction(+:eng_tmp,v0,v1,v2,v3,v4,v5) ++#pragma omp parallel default(shared) reduction(+:eng_tmp,v0,v1,v2,v3,v4,v5) + #endif + { + +@@ -234,7 +234,7 @@ + const int nthreads = comm->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int i,ifrom,ito,k,l,m,n,ic,tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_gravity_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_gravity_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_gravity_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_gravity_omp.cpp 2020-03-20 16:49:48.250419819 +0100 +@@ -69,7 +69,7 @@ + + if (rmass) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(-:grav) ++#pragma omp parallel for default(shared) reduction(-:grav) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +@@ -81,7 +81,7 @@ + } + } else { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(-:grav) ++#pragma omp parallel for default(shared) reduction(-:grav) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_neigh_history_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_neigh_history_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_neigh_history_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_neigh_history_omp.cpp 2020-03-20 16:49:48.254419839 +0100 +@@ -73,7 +73,7 @@ + maxpartner = 0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + +@@ -199,7 +199,7 @@ + for (int i = 0; i < nall_neigh; i++) npartner[i] = 0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + +@@ -373,7 +373,7 @@ + maxpartner = 0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + +@@ -525,7 +525,7 @@ + + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_asphere_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nh_asphere_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_asphere_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_nh_asphere_omp.cpp 2020-03-20 16:49:48.256419849 +0100 +@@ -82,7 +82,7 @@ + // merged with FixNHOMP instead of calling it for the COM update. + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -122,7 +122,7 @@ + // principal moments of inertia + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +@@ -163,7 +163,7 @@ + + if (which == NOBIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -177,7 +177,7 @@ + } + } else if (which == BIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + double buf[3]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nh_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_nh_omp.cpp 2020-03-20 16:49:48.259419864 +0100 +@@ -57,7 +57,7 @@ + if (allremap) domain->x2lamda(nlocal); + else { + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) +@@ -207,7 +207,7 @@ + if (allremap) domain->lamda2x(nlocal); + else { + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) +@@ -235,7 +235,7 @@ + + if (which == NOBIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -253,7 +253,7 @@ + } + } else if (which == BIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + double buf[3]; +@@ -289,7 +289,7 @@ + if (atom->rmass) { + const double * _noalias const rmass = atom->rmass; + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -303,7 +303,7 @@ + const double *_noalias const mass = atom->mass; + const int * _noalias const type = atom->type; + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -330,7 +330,7 @@ + // x update by full step only for atoms in group + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -352,7 +352,7 @@ + + if (which == NOBIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -363,7 +363,7 @@ + } + } else if (which == BIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + double buf[3]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_sphere_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nh_sphere_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nh_sphere_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_nh_sphere_omp.cpp 2020-03-20 16:49:48.262419879 +0100 +@@ -85,7 +85,7 @@ + // 4 cases depending on radius vs shape and rmass vs mass + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -115,7 +115,7 @@ + + if (which == NOBIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -129,7 +129,7 @@ + } + } else if (which == BIAS) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + double buf[3]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nve_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_nve_omp.cpp 2020-03-20 16:49:48.279419964 +0100 +@@ -41,7 +41,7 @@ + if (atom->rmass) { + const double * const rmass = atom->rmass; + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +@@ -58,7 +58,7 @@ + const double * const mass = atom->mass; + const int * const type = atom->type; + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +@@ -87,7 +87,7 @@ + if (atom->rmass) { + const double * const rmass = atom->rmass; + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +@@ -101,7 +101,7 @@ + const double * const mass = atom->mass; + const int * const type = atom->type; + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_sphere_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nve_sphere_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nve_sphere_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_nve_sphere_omp.cpp 2020-03-20 16:49:48.281419974 +0100 +@@ -49,7 +49,7 @@ + // update v,x,omega for all particles + // d_omega/dt = torque / inertia + #if defined(_OPENMP) +-#pragma omp parallel for default(none) ++#pragma omp parallel for default(shared) + #endif + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { +@@ -76,7 +76,7 @@ + double * const * const mu = atom->mu; + if (dlm == NODLM) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) ++#pragma omp parallel for default(shared) + #endif + for (int i = 0; i < nlocal; i++) { + double g0,g1,g2,msq,scale; +@@ -95,7 +95,7 @@ + } + } else { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) ++#pragma omp parallel for default(shared) + #endif + // Integrate orientation following Dullweber-Leimkuhler-Maclachlan scheme + for (int i = 0; i < nlocal; i++) { +@@ -223,7 +223,7 @@ + // d_omega/dt = torque / inertia + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) ++#pragma omp parallel for default(shared) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nvt_sllod_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_nvt_sllod_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_nvt_sllod_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_nvt_sllod_omp.cpp 2020-03-20 16:49:48.290420019 +0100 +@@ -114,7 +114,7 @@ + MathExtra::multiply_shape_shape(domain->h_rate,domain->h_inv,h_two); + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) shared(h_two) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + double vdelu0,vdelu1,vdelu2,buf[3]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_omp.cpp 2020-03-20 16:49:48.296420049 +0100 +@@ -70,7 +70,7 @@ + if (narg > 3) { + #if defined(_OPENMP) + if (strcmp(arg[3],"0") == 0) +-#pragma omp parallel default(none) shared(nthreads) ++#pragma omp parallel default(shared) + nthreads = omp_get_num_threads(); + else + nthreads = force->inumeric(FLERR,arg[3]); +@@ -134,7 +134,7 @@ + thr = new ThrData *[nthreads]; + _nthr = nthreads; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(lmp) ++#pragma omp parallel default(shared) + #endif + { + const int tid = get_tid(); +@@ -186,7 +186,7 @@ + thr = new ThrData *[nthreads]; + _nthr = nthreads; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const int tid = get_tid(); +@@ -350,7 +350,7 @@ + double *drho = atom->drho; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(f,torque,erforce,de,drho) ++#pragma omp parallel default(shared) + #endif + { + const int tid = get_tid(); +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_nh_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_nh_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_nh_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_nh_omp.cpp 2020-03-20 16:49:48.313420133 +0100 +@@ -89,7 +89,7 @@ + double akt=0.0, akr=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) shared(scale_r,scale_t,scale_v) schedule(static) reduction(+:akt,akr) ++#pragma omp parallel for default(shared) schedule(static) reduction(+:akt,akr) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + double mbody[3],tbody[3],fquat[4]; +@@ -250,7 +250,7 @@ + int i; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) private(i) reduction(+:s0,s1,s2,s3,s4,s5) ++#pragma omp parallel for default(shared) private(i) reduction(+:s0,s1,s2,s3,s4,s5) + #endif + for (i = 0; i < nlocal; i++) { + const int ibody = body[i]; +@@ -289,7 +289,7 @@ + int i; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) private(i) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5) ++#pragma omp parallel for default(shared) private(i) reduction(+:s0,s1,s2,s3,s4,s5) + #endif + for (i = 0; i < nlocal; i++) { + const int ibody = body[i]; +@@ -330,7 +330,7 @@ + memset(&sum[0][0],0,6*nbody*sizeof(double)); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -373,7 +373,7 @@ + MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) private(ibody) schedule(static) ++#pragma omp parallel for default(shared) private(ibody) schedule(static) + #endif + for (ibody = 0; ibody < nbody; ibody++) { + fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; +@@ -388,7 +388,7 @@ + + if (id_gravity) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) private(ibody) schedule(static) ++#pragma omp parallel for default(shared) private(ibody) schedule(static) + #endif + for (ibody = 0; ibody < nbody; ibody++) { + fcm[ibody][0] += gvec[0]*masstotal[ibody]; +@@ -433,7 +433,7 @@ + const double dtf2 = dtf * 2.0; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr) ++#pragma omp parallel for default(shared) schedule(static) reduction(+:akt,akr) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + double mbody[3],tbody[3],fquat[4]; +@@ -554,7 +554,7 @@ + if (allremap) domain->x2lamda(nlocal); + else { + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) +@@ -586,7 +586,7 @@ + if (allremap) domain->lamda2x(nlocal); + else { + #if defined (_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) + if (mask[i] & dilate_group_bit) +@@ -631,7 +631,7 @@ + int i; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) ++#pragma omp parallel for default(shared) private(i) reduction(+:v0,v1,v2,v3,v4,v5) + #endif + for (i = 0; i < nlocal; i++) { + const int ibody = body[i]; +@@ -832,7 +832,7 @@ + int i; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) private(i) reduction(+:v0,v1,v2,v3,v4,v5) ++#pragma omp parallel for default(shared) private(i) reduction(+:v0,v1,v2,v3,v4,v5) + #endif + for (i = 0; i < nlocal; i++) { + const int ibody = body[i]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_omp.cpp 2020-03-20 16:49:48.327420203 +0100 +@@ -47,7 +47,7 @@ + void FixRigidOMP::initial_integrate(int vflag) + { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + +@@ -120,7 +120,7 @@ + double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:s0,s1,s2,s3,s4,s5) ++#pragma omp parallel for default(shared) reduction(+:s0,s1,s2,s3,s4,s5) + #endif + for (int i = 0; i < nlocal; i++) { + const int ibody = body[i]; +@@ -158,7 +158,7 @@ + double s0=0.0,s1=0.0,s2=0.0,s3=0.0,s4=0.0,s5=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) shared(ib) reduction(+:s0,s1,s2,s3,s4,s5) ++#pragma omp parallel for default(shared) reduction(+:s0,s1,s2,s3,s4,s5) + #endif + for (int i = 0; i < nlocal; i++) { + const int ibody = body[i]; +@@ -199,7 +199,7 @@ + memset(&sum[0][0],0,6*nbody*sizeof(double)); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -246,7 +246,7 @@ + // fflag,tflag = 0 for some dimensions in 2d + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; +@@ -261,7 +261,7 @@ + + if (id_gravity) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + fcm[ibody][0] += gvec[0]*masstotal[ibody]; +@@ -280,7 +280,7 @@ + // update vcm and angmom + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + +@@ -346,7 +346,7 @@ + const int nlocal = atom->nlocal; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) ++#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) + #endif + for (int i = 0; i < nlocal; i++) { + const int ibody = body[i]; +@@ -546,7 +546,7 @@ + const int nlocal = atom->nlocal; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) ++#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) + #endif + for (int i = 0; i < nlocal; i++) { + const int ibody = body[i]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_small_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_small_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/fix_rigid_small_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/fix_rigid_small_omp.cpp 2020-03-20 16:49:48.331420223 +0100 +@@ -46,7 +46,7 @@ + { + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nlocal_body; ibody++) { + +@@ -117,7 +117,7 @@ + const int nthreads=comm->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nlocal_body+nghost_body; ibody++) { + double * _noalias const fcm = body[ibody].fcm; +@@ -132,7 +132,7 @@ + // and then each thread only processes some bodies. + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -183,7 +183,7 @@ + + if (langflag) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nlocal_body; ibody++) { + double * _noalias const fcm = body[ibody].fcm; +@@ -201,7 +201,7 @@ + + if (id_gravity) { + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nbody; ibody++) { + double * _noalias const fcm = body[ibody].fcm; +@@ -222,7 +222,7 @@ + // update vcm and angmom, recompute omega + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) schedule(static) ++#pragma omp parallel for default(shared) schedule(static) + #endif + for (int ibody = 0; ibody < nlocal_body; ibody++) { + Body &b = body[ibody]; +@@ -294,7 +294,7 @@ + const int nlocal = atom->nlocal; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) ++#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) + #endif + for (int i = 0; i < nlocal; i++) { + const int ibody = atom2body[i]; +@@ -489,7 +489,7 @@ + const int nlocal = atom->nlocal; + + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:v0,v1,v2,v3,v4,v5) ++#pragma omp parallel for default(shared) reduction(+:v0,v1,v2,v3,v4,v5) + #endif + for (int i = 0; i < nlocal; i++) { + const int ibody = atom2body[i]; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_class2_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_class2_omp.cpp 2020-03-20 16:49:48.336420248 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cossq_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_cossq_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cossq_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_cossq_omp.cpp 2020-03-20 16:49:48.339420263 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cvff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_cvff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_cvff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_cvff_omp.cpp 2020-03-20 16:49:48.342420278 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_fourier_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_fourier_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_fourier_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_fourier_omp.cpp 2020-03-20 16:49:48.346420298 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_harmonic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_harmonic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_harmonic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_harmonic_omp.cpp 2020-03-20 16:49:48.348420308 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_ring_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_ring_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_ring_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_ring_omp.cpp 2020-03-20 16:49:48.351420323 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/improper_umbrella_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/improper_umbrella_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/improper_umbrella_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/improper_umbrella_omp.cpp 2020-03-20 16:49:48.354420338 +0100 +@@ -50,7 +50,7 @@ + const int inum = neighbor->nimproperlist; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/msm_cg_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/msm_cg_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/msm_cg_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/msm_cg_omp.cpp 2020-03-20 16:49:48.358420358 +0100 +@@ -310,7 +310,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/msm_omp.cpp 2020-03-20 16:49:48.362420378 +0100 +@@ -52,7 +52,7 @@ + MSM::compute(eflag,vflag); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -158,7 +158,7 @@ + const int n=nn; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) reduction(+:v0,v1,v2,v3,v4,v5,emsm) ++#pragma omp parallel default(shared) reduction(+:v0,v1,v2,v3,v4,v5,emsm) + #endif + { + double esum,v0sum,v1sum,v2sum,v3sum,v4sum,v5sum; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_atomonly_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_atomonly_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_atomonly_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_atomonly_omp.cpp 2020-03-20 16:49:48.364420388 +0100 +@@ -36,7 +36,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_ghost_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_ghost_omp.cpp 2020-03-20 16:49:48.367420403 +0100 +@@ -42,7 +42,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nall); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_bin_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_bin_omp.cpp 2020-03-20 16:49:48.369420413 +0100 +@@ -40,7 +40,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_multi_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_multi_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_multi_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_multi_omp.cpp 2020-03-20 16:49:48.372420428 +0100 +@@ -41,7 +41,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_ghost_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_ghost_omp.cpp 2020-03-20 16:49:48.375420443 +0100 +@@ -42,7 +42,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nall); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_full_nsq_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_full_nsq_omp.cpp 2020-03-20 16:49:48.378420458 +0100 +@@ -42,7 +42,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_atomonly_newton_omp.cpp 2020-03-20 16:49:48.381420473 +0100 +@@ -37,7 +37,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp 2020-03-20 16:49:48.384420487 +0100 +@@ -46,7 +46,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nall); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newtoff_omp.cpp 2020-03-20 16:49:48.387420503 +0100 +@@ -42,7 +42,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_omp.cpp 2020-03-20 16:49:48.390420517 +0100 +@@ -41,7 +41,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp 2020-03-20 16:49:48.392420527 +0100 +@@ -41,7 +41,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newtoff_omp.cpp 2020-03-20 16:49:48.395420542 +0100 +@@ -38,7 +38,7 @@ + NPAIR_OMP_INIT; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(inum_full); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_halffull_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_halffull_newton_omp.cpp 2020-03-20 16:49:48.398420557 +0100 +@@ -38,7 +38,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(inum_full); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newtoff_omp.cpp 2020-03-20 16:49:48.401420572 +0100 +@@ -43,7 +43,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_omp.cpp 2020-03-20 16:49:48.404420587 +0100 +@@ -42,7 +42,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp 2020-03-20 16:49:48.407420602 +0100 +@@ -43,7 +43,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_ghost_omp.cpp 2020-03-20 16:49:48.409420612 +0100 +@@ -47,7 +47,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nall); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newtoff_omp.cpp 2020-03-20 16:49:48.412420627 +0100 +@@ -44,7 +44,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_nsq_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_nsq_newton_omp.cpp 2020-03-20 16:49:48.415420642 +0100 +@@ -43,7 +43,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp 2020-03-20 16:49:48.417420652 +0100 +@@ -47,7 +47,7 @@ + const int respamiddle = list->respamiddle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp 2020-03-20 16:49:48.421420672 +0100 +@@ -46,7 +46,7 @@ + const int respamiddle = list->respamiddle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp 2020-03-20 16:49:48.423420682 +0100 +@@ -46,7 +46,7 @@ + const int respamiddle = list->respamiddle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp 2020-03-20 16:49:48.426420697 +0100 +@@ -48,7 +48,7 @@ + const int respamiddle = list->respamiddle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp 2020-03-20 16:49:48.429420712 +0100 +@@ -49,7 +49,7 @@ + const int respamiddle = list->respamiddle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp 2020-03-20 16:49:48.432420727 +0100 +@@ -43,7 +43,7 @@ + NPAIR_OMP_INIT; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_omp.cpp 2020-03-20 16:49:48.435420742 +0100 +@@ -42,7 +42,7 @@ + NPAIR_OMP_INIT; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp 2020-03-20 16:49:48.437420752 +0100 +@@ -41,7 +41,7 @@ + + NPAIR_OMP_INIT; + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp 2020-03-20 16:49:48.440420767 +0100 +@@ -45,7 +45,7 @@ + NPAIR_OMP_INIT; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp 2020-03-20 16:49:48.442420777 +0100 +@@ -46,7 +46,7 @@ + NPAIR_OMP_INIT; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(list) ++#pragma omp parallel default(shared) + #endif + NPAIR_OMP_SETUP(nlocal); + +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_adp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_adp_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_adp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_adp_omp.cpp 2020-03-20 16:49:48.446420797 +0100 +@@ -62,7 +62,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_agni_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_agni_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_agni_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_agni_omp.cpp 2020-03-20 16:49:48.449420812 +0100 +@@ -49,7 +49,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_airebo_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_airebo_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_airebo_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_airebo_omp.cpp 2020-03-20 16:49:48.461420871 +0100 +@@ -58,7 +58,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) reduction(+:pv0,pv1,pv2) ++#pragma omp parallel default(shared) reduction(+:pv0,pv1,pv2) + #endif + { + int ifrom, ito, tid; +@@ -104,7 +104,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int i,j,ii,jj,n,jnum,itype,jtype; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_beck_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_beck_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_beck_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_beck_omp.cpp 2020-03-20 16:49:48.464420887 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_long_omp.cpp 2020-03-20 16:49:48.467420901 +0100 +@@ -51,7 +51,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_msm_omp.cpp 2020-03-20 16:49:48.470420916 +0100 +@@ -48,7 +48,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_wolf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_wolf_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_coul_wolf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_coul_wolf_omp.cpp 2020-03-20 16:49:48.474420936 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_born_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_born_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_born_omp.cpp 2020-03-20 16:49:48.477420951 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_omp.cpp 2020-03-20 16:49:48.480420966 +0100 +@@ -135,7 +135,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_poly_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_poly_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_brownian_poly_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_brownian_poly_omp.cpp 2020-03-20 16:49:48.484420986 +0100 +@@ -135,7 +135,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_cut_omp.cpp 2020-03-20 16:49:48.486420996 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_long_omp.cpp 2020-03-20 16:49:48.489421011 +0100 +@@ -51,7 +51,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_coul_msm_omp.cpp 2020-03-20 16:49:48.492421026 +0100 +@@ -48,7 +48,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_long_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_long_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_long_coul_long_omp.cpp 2020-03-20 16:49:48.497421051 +0100 +@@ -56,7 +56,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -320,7 +320,7 @@ + const int nthreads = comm->nthreads; + const int inum = list->inum_inner; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -345,7 +345,7 @@ + const int inum = list->inum_middle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -375,7 +375,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_buck_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_buck_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_buck_omp.cpp 2020-03-20 16:49:48.500421066 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_colloid_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_colloid_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_colloid_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_colloid_omp.cpp 2020-03-20 16:49:48.503421081 +0100 +@@ -46,7 +46,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_comb_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_comb_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_comb_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_comb_omp.cpp 2020-03-20 16:49:48.507421101 +0100 +@@ -52,7 +52,7 @@ + Short_neigh_thr(); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -411,7 +411,7 @@ + + // loop over full neighbor list of my atoms + #if defined(_OPENMP) +-#pragma omp parallel for private(ii) default(none) shared(potal,fac11e) ++#pragma omp parallel for private(ii) default(shared) + #endif + for (ii = 0; ii < inum; ii ++) { + double fqi,fqj,fqij,fqji,fqjj,delr1[3]; +@@ -564,7 +564,7 @@ + const int nthreads = comm->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int nj,*neighptrj; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_omp.cpp 2020-03-20 16:49:48.510421116 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_cut_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_cut_soft_omp.cpp 2020-03-20 16:49:48.512421126 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_debye_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_debye_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_debye_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_debye_omp.cpp 2020-03-20 16:49:48.515421141 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_diel_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_diel_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_diel_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_diel_omp.cpp 2020-03-20 16:49:48.517421151 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_dsf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_dsf_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_dsf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_dsf_omp.cpp 2020-03-20 16:49:48.520421166 +0100 +@@ -52,7 +52,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_omp.cpp 2020-03-20 16:49:48.523421181 +0100 +@@ -52,7 +52,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_long_soft_omp.cpp 2020-03-20 16:49:48.526421196 +0100 +@@ -51,7 +51,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_msm_omp.cpp 2020-03-20 16:49:48.529421211 +0100 +@@ -49,7 +49,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_wolf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_coul_wolf_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_coul_wolf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_coul_wolf_omp.cpp 2020-03-20 16:49:48.531421220 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_omp.cpp 2020-03-20 16:49:48.535421241 +0100 +@@ -80,7 +80,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_tstat_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_tstat_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_dpd_tstat_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_dpd_tstat_omp.cpp 2020-03-20 16:49:48.538421255 +0100 +@@ -79,7 +79,7 @@ + random_thr[0] = random; + } + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_cd_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_eam_cd_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_cd_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_eam_cd_omp.cpp 2020-03-20 16:49:48.545421290 +0100 +@@ -77,7 +77,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_eam_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eam_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_eam_omp.cpp 2020-03-20 16:49:48.551421320 +0100 +@@ -59,7 +59,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_edip_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_edip_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_edip_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_edip_omp.cpp 2020-03-20 16:49:48.555421340 +0100 +@@ -50,7 +50,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eim_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_eim_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_eim_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_eim_omp.cpp 2020-03-20 16:49:48.558421355 +0100 +@@ -57,7 +57,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_cut_omp.cpp 2020-03-20 16:49:48.561421370 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gauss_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_gauss_omp.cpp 2020-03-20 16:49:48.563421380 +0100 +@@ -45,7 +45,7 @@ + double occ = 0.0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) reduction(+:occ) ++#pragma omp parallel default(shared) reduction(+:occ) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gayberne_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gayberne_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gayberne_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_gayberne_omp.cpp 2020-03-20 16:49:48.566421395 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hertz_history_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hertz_history_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hertz_history_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hertz_history_omp.cpp 2020-03-20 16:49:48.569421410 +0100 +@@ -69,7 +69,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_history_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_history_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_history_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_history_omp.cpp 2020-03-20 16:49:48.572421425 +0100 +@@ -70,7 +70,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_gran_hooke_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_gran_hooke_omp.cpp 2020-03-20 16:49:48.575421440 +0100 +@@ -65,7 +65,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp 2020-03-20 16:49:48.578421455 +0100 +@@ -74,7 +74,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp 2020-03-20 16:49:48.581421470 +0100 +@@ -74,7 +74,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj96_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj96_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj96_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj96_cut_omp.cpp 2020-03-20 16:49:48.584421485 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp 2020-03-20 16:49:48.586421495 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp 2020-03-20 16:49:48.589421510 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp 2020-03-20 16:49:48.592421525 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp 2020-03-20 16:49:48.595421540 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp 2020-03-20 16:49:48.597421550 +0100 +@@ -49,7 +49,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp 2020-03-20 16:49:48.601421569 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp 2020-03-20 16:49:48.605421590 +0100 +@@ -51,7 +51,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_class2_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_class2_omp.cpp 2020-03-20 16:49:48.608421604 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cubic_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cubic_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cubic_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cubic_omp.cpp 2020-03-20 16:49:48.611421620 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp 2020-03-20 16:49:48.614421634 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp 2020-03-20 16:49:48.617421649 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp 2020-03-20 16:49:48.619421659 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp 2020-03-20 16:49:48.622421674 +0100 +@@ -53,7 +53,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp 2020-03-20 16:49:48.625421689 +0100 +@@ -52,7 +52,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp 2020-03-20 16:49:48.628421704 +0100 +@@ -52,7 +52,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp 2020-03-20 16:49:48.632421724 +0100 +@@ -49,7 +49,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp 2020-03-20 16:49:48.635421739 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp 2020-03-20 16:49:48.639421759 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_omp.cpp 2020-03-20 16:49:48.642421774 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_soft_omp.cpp 2020-03-20 16:49:48.645421789 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp 2020-03-20 16:49:48.648421804 +0100 +@@ -70,7 +70,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp 2020-03-20 16:49:48.652421824 +0100 +@@ -93,7 +93,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp 2020-03-20 16:49:48.657421849 +0100 +@@ -93,7 +93,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp 2020-03-20 16:49:48.661421869 +0100 +@@ -93,7 +93,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_expand_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_expand_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_expand_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_expand_omp.cpp 2020-03-20 16:49:48.665421889 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp 2020-03-20 16:49:48.669421909 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_gromacs_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_gromacs_omp.cpp 2020-03-20 16:49:48.673421929 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_coul_long_omp.cpp 2020-03-20 16:49:48.681421968 +0100 +@@ -56,7 +56,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -318,7 +318,7 @@ + const int nthreads = comm->nthreads; + const int inum = list->inum_inner; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -343,7 +343,7 @@ + const int inum = list->inum_middle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -373,7 +373,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp 2020-03-20 16:49:48.692422023 +0100 +@@ -96,7 +96,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -379,7 +379,7 @@ + const int nthreads = comm->nthreads; + const int inum = list->inum_inner; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -404,7 +404,7 @@ + const int inum = list->inum_middle; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +@@ -458,7 +458,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp 2020-03-20 16:49:48.695422038 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp 2020-03-20 16:49:48.698422053 +0100 +@@ -51,7 +51,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sdk_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sdk_omp.cpp 2020-03-20 16:49:48.701422068 +0100 +@@ -47,7 +47,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp 2020-03-20 16:49:48.704422083 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_linear_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_linear_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_linear_omp.cpp 2020-03-20 16:49:48.707422098 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lj_smooth_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lj_smooth_omp.cpp 2020-03-20 16:49:48.709422108 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_omp.cpp 2020-03-20 16:49:48.713422128 +0100 +@@ -109,7 +109,7 @@ + + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_poly_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_poly_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_lubricate_poly_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_lubricate_poly_omp.cpp 2020-03-20 16:49:48.717422148 +0100 +@@ -106,7 +106,7 @@ + + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_meam_spline_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_meam_spline_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_meam_spline_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_meam_spline_omp.cpp 2020-03-20 16:49:48.721422168 +0100 +@@ -57,7 +57,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_morse_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_morse_omp.cpp 2020-03-20 16:49:48.724422183 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_smooth_linear_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_morse_smooth_linear_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_morse_smooth_linear_omp.cpp 2020-03-20 16:49:48.727422198 +0100 +@@ -47,7 +47,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp 2020-03-20 16:49:48.731422218 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp 2020-03-20 16:49:48.735422238 +0100 +@@ -51,7 +51,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_nm_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_nm_cut_omp.cpp 2020-03-20 16:49:48.737422248 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_lps_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_peri_lps_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_lps_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_peri_lps_omp.cpp 2020-03-20 16:49:48.741422268 +0100 +@@ -62,7 +62,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_pmb_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_peri_pmb_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_peri_pmb_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_peri_pmb_omp.cpp 2020-03-20 16:49:48.744422283 +0100 +@@ -58,7 +58,7 @@ + } + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_resquared_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_resquared_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_resquared_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_resquared_omp.cpp 2020-03-20 16:49:48.754422332 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_soft_omp.cpp 2020-03-20 16:49:48.756422342 +0100 +@@ -47,7 +47,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_sw_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_sw_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_sw_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_sw_omp.cpp 2020-03-20 16:49:48.759422358 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_table_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_table_omp.cpp 2020-03-20 16:49:48.762422372 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_c_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_c_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_c_omp.cpp 2020-03-20 16:49:48.765422388 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_mod_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_mod_omp.cpp 2020-03-20 16:49:48.768422402 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_omp.cpp 2020-03-20 16:49:48.772422422 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_table_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tersoff_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tersoff_table_omp.cpp 2020-03-20 16:49:48.776422442 +0100 +@@ -68,7 +68,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_cut_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_cut_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_cut_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_cut_omp.cpp 2020-03-20 16:49:48.784422482 +0100 +@@ -92,7 +92,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_omp.cpp 2020-03-20 16:49:48.789422507 +0100 +@@ -93,7 +93,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_soft_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_soft_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_tip4p_long_soft_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_tip4p_long_soft_omp.cpp 2020-03-20 16:49:48.794422532 +0100 +@@ -93,7 +93,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_ufm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_ufm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_ufm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_ufm_omp.cpp 2020-03-20 16:49:48.798422552 +0100 +@@ -45,7 +45,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_omp.cpp 2020-03-20 16:49:48.802422572 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_table_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_table_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_vashishta_table_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_vashishta_table_omp.cpp 2020-03-20 16:49:48.806422592 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_colloid_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_colloid_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_colloid_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_colloid_omp.cpp 2020-03-20 16:49:48.809422607 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_yukawa_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_yukawa_omp.cpp 2020-03-20 16:49:48.813422627 +0100 +@@ -43,7 +43,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pair_zbl_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pair_zbl_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pair_zbl_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pair_zbl_omp.cpp 2020-03-20 16:49:48.817422647 +0100 +@@ -44,7 +44,7 @@ + const int inum = list->inum; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + int ifrom, ito, tid; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_cg_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_cg_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_cg_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pppm_cg_omp.cpp 2020-03-20 16:49:48.823422677 +0100 +@@ -59,7 +59,7 @@ + PPPMCGOMP::~PPPMCGOMP() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -81,7 +81,7 @@ + PPPMCG::allocate(); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -122,7 +122,7 @@ + const int twoorder = 2*order; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double snx,sny,snz; +@@ -216,7 +216,7 @@ + double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) ++#pragma omp parallel default(shared) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) + #endif + { + double snx,sny,snz,sqk; +@@ -314,7 +314,7 @@ + PPPMCG::compute(eflag,vflag); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -351,7 +351,7 @@ + const int iy = nyhi_out - nylo_out + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const double * _noalias const q = atom->q; +@@ -443,7 +443,7 @@ + const int nthreads = comm->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + FFT_SCALAR dx,dy,dz,x0,y0,z0,ekx,eky,ekz; +@@ -524,7 +524,7 @@ + const int nthreads = comm->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + int i,ifrom,ito,tid,l,m,n,nx,ny,nz,mx,my,mz; +@@ -617,7 +617,7 @@ + const int nthreads = comm->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + FFT_SCALAR dx,dy,dz,x0,y0,z0; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_omp.cpp 2020-03-20 16:49:48.831422716 +0100 +@@ -59,7 +59,7 @@ + PPPMDispOMP::~PPPMDispOMP() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -87,7 +87,7 @@ + PPPMDisp::allocate(); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -114,7 +114,7 @@ + void PPPMDispOMP::compute_gf() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + +@@ -204,7 +204,7 @@ + void PPPMDispOMP::compute_gf_6() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double *prd; +@@ -311,7 +311,7 @@ + + PPPMDisp::compute(eflag,vflag); + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -366,7 +366,7 @@ + + int flag = 0; + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:flag) schedule(static) ++#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + +@@ -419,7 +419,7 @@ + const int iy = nyhi_out - nylo_out + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const double * _noalias const q = atom->q; +@@ -509,7 +509,7 @@ + const int iy = nyhi_out_6 - nylo_out_6 + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; +@@ -613,7 +613,7 @@ + const int iy = nyhi_out_6 - nylo_out_6 + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; +@@ -723,7 +723,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -828,7 +828,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -935,7 +935,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1034,7 +1034,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1138,7 +1138,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1248,7 +1248,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1350,7 +1350,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1486,7 +1486,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1663,7 +1663,7 @@ + + #if defined(_OPENMP) + const int nthreads = comm->nthreads; +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_tip4p_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_tip4p_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_disp_tip4p_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pppm_disp_tip4p_omp.cpp 2020-03-20 16:49:48.839422756 +0100 +@@ -56,7 +56,7 @@ + { + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -84,7 +84,7 @@ + PPPMDispTIP4P::allocate(); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -111,7 +111,7 @@ + void PPPMDispTIP4POMP::compute_gf() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + +@@ -198,7 +198,7 @@ + void PPPMDispTIP4POMP::compute_gf_6() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double *prd; +@@ -302,7 +302,7 @@ + PPPMDispTIP4P::compute(eflag,vflag); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -358,7 +358,7 @@ + + int flag = 0; + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:flag) schedule(static) ++#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + dbl3_t xM; +@@ -434,7 +434,7 @@ + + int flag = 0; + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:flag) schedule(static) ++#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + +@@ -487,7 +487,7 @@ + const int iy = nyhi_out - nylo_out + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const double * _noalias const q = atom->q; +@@ -582,7 +582,7 @@ + const int iy = nyhi_out_6 - nylo_out_6 + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; +@@ -684,7 +684,7 @@ + const int iy = nyhi_out_6 - nylo_out_6 + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; +@@ -795,7 +795,7 @@ + const double boxloz = boxlo[2]; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + dbl3_t xM; +@@ -903,7 +903,7 @@ + const double boxloz = boxlo[2]; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double s1,s2,s3,sf; +@@ -1018,7 +1018,7 @@ + const double * const * const x = atom->x; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1119,7 +1119,7 @@ + const double hz_inv = nz_pppm_6/zprd_slab; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1226,7 +1226,7 @@ + const double * const * const x = atom->x; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1325,7 +1325,7 @@ + const double * const * const x = atom->x; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1458,7 +1458,7 @@ + const double hz_inv = nz_pppm_6/zprd_slab; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -1632,7 +1632,7 @@ + const double * const * const x = atom->x; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pppm_omp.cpp 2020-03-20 16:49:48.845422786 +0100 +@@ -61,7 +61,7 @@ + PPPM::allocate(); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -81,7 +81,7 @@ + PPPMOMP::~PPPMOMP() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -122,7 +122,7 @@ + const int twoorder = 2*order; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double snx,sny,snz; +@@ -216,7 +216,7 @@ + double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) ++#pragma omp parallel default(shared) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) + #endif + { + double snx,sny,snz,sqk; +@@ -314,7 +314,7 @@ + PPPM::compute(eflag,vflag); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -352,7 +352,7 @@ + const int iy = nyhi_out - nylo_out + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const double * _noalias const q = atom->q; +@@ -449,7 +449,7 @@ + const double boxloz = boxlo[2]; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + FFT_SCALAR x0,y0,z0,ekx,eky,ekz; +@@ -534,7 +534,7 @@ + const double boxloz = boxlo[2]; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double s1,s2,s3,sf; +@@ -627,7 +627,7 @@ + const double * _noalias const q = atom->q; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + FFT_SCALAR dx,dy,dz,x0,y0,z0; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_tip4p_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/pppm_tip4p_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/pppm_tip4p_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/pppm_tip4p_omp.cpp 2020-03-20 16:49:48.851422816 +0100 +@@ -61,7 +61,7 @@ + PPPMTIP4POMP::~PPPMTIP4POMP() + { + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -83,7 +83,7 @@ + PPPMTIP4P::allocate(); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -124,7 +124,7 @@ + const int twoorder = 2*order; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double snx,sny,snz; +@@ -218,7 +218,7 @@ + double sf0=0.0,sf1=0.0,sf2=0.0,sf3=0.0,sf4=0.0,sf5=0.0; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) ++#pragma omp parallel default(shared) reduction(+:sf0,sf1,sf2,sf3,sf4,sf5) + #endif + { + double snx,sny,snz,sqk; +@@ -316,7 +316,7 @@ + PPPMTIP4P::compute(eflag,vflag); + + #if defined(_OPENMP) +-#pragma omp parallel default(none) shared(eflag,vflag) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -355,7 +355,7 @@ + + int flag = 0; + #if defined(_OPENMP) +-#pragma omp parallel for default(none) reduction(+:flag) schedule(static) ++#pragma omp parallel for default(shared) reduction(+:flag) schedule(static) + #endif + for (int i = 0; i < nlocal; i++) { + dbl3_t xM; +@@ -416,7 +416,7 @@ + const int iy = nyhi_out - nylo_out + 1; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + const double * _noalias const q = atom->q; +@@ -521,7 +521,7 @@ + const double boxloz = boxlo[2]; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + dbl3_t xM; +@@ -632,7 +632,7 @@ + const double boxloz = boxlo[2]; + + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + double s1,s2,s3,sf; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_forces_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/reaxc_forces_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_forces_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/reaxc_forces_omp.cpp 2020-03-20 16:49:48.863422876 +0100 +@@ -146,7 +146,7 @@ + reax_list *bonds = (*lists) + BONDS; + + #if defined(_OPENMP) +-#pragma omp parallel default(shared) //default(none) ++#pragma omp parallel default(shared) //default(shared) + #endif + { + int i, j, k, pj, pk, start_j, end_j; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp 2020-03-20 16:49:48.867422896 +0100 +@@ -57,7 +57,7 @@ + const int nthreads = control->nthreads; + + #if defined(_OPENMP) +-#pragma omp parallel default(shared) //default(none) ++#pragma omp parallel default(shared) //default(shared) + #endif + { + int i, j, k, pi, pk; +diff -Nru lammps-stable_3Mar2020.orig/src/USER-OMP/respa_omp.cpp lammps-stable_3Mar2020/src/USER-OMP/respa_omp.cpp +--- lammps-stable_3Mar2020.orig/src/USER-OMP/respa_omp.cpp 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/USER-OMP/respa_omp.cpp 2020-03-20 16:49:48.887422996 +0100 +@@ -146,7 +146,7 @@ + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -241,7 +241,7 @@ + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) +@@ -394,7 +394,7 @@ + const int nall = atom->nlocal + atom->nghost; + const int nthreads = comm->nthreads; + #if defined(_OPENMP) +-#pragma omp parallel default(none) ++#pragma omp parallel default(shared) + #endif + { + #if defined(_OPENMP) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..8e0da02f6d7 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.5_deprecated_time_method.patch'] +checksums = [ + '69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c', # molmod-1.4.5.tar.gz + '7de0dae2accd908ff7b40f5f848ffabdb9267dadbfb8cc4d2d98444995282e2d', # molmod-1.4.5_deprecated_time_method.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..369862bf7c7 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.5_deprecated_time_method.patch'] +checksums = [ + '69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c', # molmod-1.4.5.tar.gz + '7de0dae2accd908ff7b40f5f848ffabdb9267dadbfb8cc4d2d98444995282e2d', # molmod-1.4.5_deprecated_time_method.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch new file mode 100644 index 00000000000..33594754c11 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch @@ -0,0 +1,42 @@ +Molmod is not compatible with Python 3.8 due to its deprecated +use of time.clock() (which is no longer supported as of 3.8) + +Alan O'Cais, 20200324 +diff -Nru molmod-1.4.5.orig/molmod/log.py molmod-1.4.5/molmod/log.py +--- molmod-1.4.5.orig/molmod/log.py 2019-09-11 20:34:14.000000000 +0200 ++++ molmod-1.4.5/molmod/log.py 2020-03-20 10:05:41.874916780 +0100 +@@ -388,11 +388,11 @@ + + def start(self): + assert self._start is None +- self._start = time.clock() ++ self._start = time.process_time() + + def stop(self): + assert self._start is not None +- self.cpu += time.clock() - self._start ++ self.cpu += time.process_time() - self._start + self._start = None + + +diff -Nru molmod-1.4.5.orig/molmod/minimizer.py molmod-1.4.5/molmod/minimizer.py +--- molmod-1.4.5.orig/molmod/minimizer.py 2019-09-11 20:34:14.000000000 +0200 ++++ molmod-1.4.5/molmod/minimizer.py 2020-03-20 10:06:39.712207523 +0100 +@@ -1414,7 +1414,7 @@ + except ConstraintError: + self._screen("CONSTRAINT PROJECT FAILED", newline=True) + return False +- self.last_end = time.clock() ++ self.last_end = time.process_time() + + def propagate(self): + # compute the new direction +@@ -1474,7 +1474,7 @@ + else: + converged = False + # timing +- end = time.clock() ++ end = time.process_time() + self._screen("%5.2f" % (end - self.last_end), newline=True) + self.last_end = end + # check convergence, part 2 diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..c2405e32d68 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..07c6e727d9e --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,60 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['8a760a637225eeb97e84b748e992ebc0730f71cdb4737af545445132380bfff9'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Boost', '1.72.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..c7b659d56d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,60 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['8a760a637225eeb97e84b748e992ebc0730f71cdb4737af545445132380bfff9'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Boost', '1.72.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb new file mode 100644 index 00000000000..b81b63698e1 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.1' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.0'), + ('GSL', '2.6'), +] + +preconfigopts = 'unset F77 && ' + +configopts = '--enable-shared --enable-static --disable-doc ' +# Tell it where to find FFTW +configopts += '--with-fftw3-includedir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb new file mode 100644 index 00000000000..7898a906584 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-intel-2020a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.1' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.0'), + ('GSL', '2.6'), +] + +preconfigopts = 'unset F77 && ' + +configopts = '--enable-shared --enable-static --disable-doc ' +# Tell it where to find FFTW +configopts += '--with-fftw3-includedir=$FFTW_INC_DIR --with-fftw3-libdir=$FFTW_LIB_DIR ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb new file mode 100755 index 00000000000..3bec1f83360 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.10.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'scikit-build' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7342017cc82dd6178e3b19377389b8a8d1f8b429d9cdb315cfb1094e34a0f526'] + +dependencies = [ + ('Python', '3.8.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'skbuild'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..268ad67bac1 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,97 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz + 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('XZ', '5.2.5'), + ('HDF5', '1.10.6'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20200222'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1b0e8c36287 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,97 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz + 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('XZ', '5.2.5'), + ('HDF5', '1.10.6'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20200222'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch b/easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch new file mode 100644 index 00000000000..60134b1fee1 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch @@ -0,0 +1,176 @@ +From 257b9d7b18d5f3db3fe099dc18f230e23f7dfbab Mon Sep 17 00:00:00 2001 +From: David Gobbi +Date: Tue, 20 Aug 2019 17:02:24 -0600 +Subject: [PATCH] Compatibility for Python 3.8 + +The PyTypeObject struct was modified in Python 3.8, this change is +required to avoid compile errors. +--- + .../PythonInterpreter/vtkPythonStdStreamCaptureHelper.h | 6 ++++++ + Wrapping/PythonCore/PyVTKMethodDescriptor.cxx | 2 +- + Wrapping/PythonCore/PyVTKNamespace.cxx | 2 +- + Wrapping/PythonCore/PyVTKReference.cxx | 8 ++++---- + Wrapping/PythonCore/PyVTKTemplate.cxx | 2 +- + Wrapping/PythonCore/vtkPythonCompatibility.h | 8 +++++++- + Wrapping/Tools/vtkWrapPythonClass.c | 2 +- + Wrapping/Tools/vtkWrapPythonEnum.c | 2 +- + Wrapping/Tools/vtkWrapPythonType.c | 2 +- + 9 files changed, 23 insertions(+), 11 deletions(-) + +diff --git a/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h b/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h +index b1c12c83de..14ccfbe928 100644 +--- a/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h ++++ b/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h +@@ -140,6 +140,12 @@ static PyTypeObject vtkPythonStdStreamCaptureHelperType = { + #if PY_VERSION_HEX >= 0x03040000 + 0, // tp_finalize + #endif ++#if PY_VERSION_HEX >= 0x03080000 ++ 0, // tp_vectorcall ++#if PY_VERSION_HEX < 0x03090000 ++ 0, // tp_print ++#endif ++#endif + }; + + static PyObject* vtkWrite(PyObject* self, PyObject* args) +diff --git a/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx b/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx +index 2b0d443537..3840038498 100644 +--- a/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx ++++ b/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx +@@ -186,7 +186,7 @@ PyTypeObject PyVTKMethodDescriptor_Type = { + sizeof(PyMethodDescrObject), // tp_basicsize + 0, // tp_itemsize + PyVTKMethodDescriptor_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/PyVTKNamespace.cxx b/Wrapping/PythonCore/PyVTKNamespace.cxx +index 71ee2a3516..5cf5bfbe6b 100644 +--- a/Wrapping/PythonCore/PyVTKNamespace.cxx ++++ b/Wrapping/PythonCore/PyVTKNamespace.cxx +@@ -49,7 +49,7 @@ PyTypeObject PyVTKNamespace_Type = { + 0, // tp_basicsize + 0, // tp_itemsize + PyVTKNamespace_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/PyVTKReference.cxx b/Wrapping/PythonCore/PyVTKReference.cxx +index 943ac71080..b7104091c0 100644 +--- a/Wrapping/PythonCore/PyVTKReference.cxx ++++ b/Wrapping/PythonCore/PyVTKReference.cxx +@@ -1010,7 +1010,7 @@ PyTypeObject PyVTKReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +@@ -1067,7 +1067,7 @@ PyTypeObject PyVTKNumberReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +@@ -1124,7 +1124,7 @@ PyTypeObject PyVTKStringReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +@@ -1181,7 +1181,7 @@ PyTypeObject PyVTKTupleReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/PyVTKTemplate.cxx b/Wrapping/PythonCore/PyVTKTemplate.cxx +index be200985b3..340fe7953b 100644 +--- a/Wrapping/PythonCore/PyVTKTemplate.cxx ++++ b/Wrapping/PythonCore/PyVTKTemplate.cxx +@@ -268,7 +268,7 @@ PyTypeObject PyVTKTemplate_Type = { + 0, // tp_basicsize + 0, // tp_itemsize + nullptr, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/vtkPythonCompatibility.h b/Wrapping/PythonCore/vtkPythonCompatibility.h +index 4a767844a6..be208faeef 100644 +--- a/Wrapping/PythonCore/vtkPythonCompatibility.h ++++ b/Wrapping/PythonCore/vtkPythonCompatibility.h +@@ -64,7 +64,13 @@ + #endif + + // PyTypeObject compatibility +-#if PY_VERSION_HEX >= 0x03040000 ++#if PY_VERSION_HEX >= 0x03090000 ++#define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \ ++ 0, 0, 0, 0, ++#elif PY_VERSION_HEX >= 0x03080000 ++#define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \ ++ 0, 0, 0, 0, 0, ++#elif PY_VERSION_HEX >= 0x03040000 + #define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \ + 0, 0, 0, + #else +diff --git a/Wrapping/Tools/vtkWrapPythonClass.c b/Wrapping/Tools/vtkWrapPythonClass.c +index b1e45f8e80..4d558ea081 100644 +--- a/Wrapping/Tools/vtkWrapPythonClass.c ++++ b/Wrapping/Tools/vtkWrapPythonClass.c +@@ -521,7 +521,7 @@ void vtkWrapPython_GenerateObjectType( + " sizeof(PyVTKObject), // tp_basicsize\n" + " 0, // tp_itemsize\n" + " PyVTKObject_Delete, // tp_dealloc\n" +- " nullptr, // tp_print\n" ++ " 0, // tp_vectorcall_offset\n" + " nullptr, // tp_getattr\n" + " nullptr, // tp_setattr\n" + " nullptr, // tp_compare\n" +diff --git a/Wrapping/Tools/vtkWrapPythonEnum.c b/Wrapping/Tools/vtkWrapPythonEnum.c +index b933702242..1249362854 100644 +--- a/Wrapping/Tools/vtkWrapPythonEnum.c ++++ b/Wrapping/Tools/vtkWrapPythonEnum.c +@@ -145,7 +145,7 @@ void vtkWrapPython_GenerateEnumType( + " sizeof(PyIntObject), // tp_basicsize\n" + " 0, // tp_itemsize\n" + " nullptr, // tp_dealloc\n" +- " nullptr, // tp_print\n" ++ " 0, // tp_vectorcall_offset\n" + " nullptr, // tp_getattr\n" + " nullptr, // tp_setattr\n" + " nullptr, // tp_compare\n" +diff --git a/Wrapping/Tools/vtkWrapPythonType.c b/Wrapping/Tools/vtkWrapPythonType.c +index 744cb1b9d3..0a1375e541 100644 +--- a/Wrapping/Tools/vtkWrapPythonType.c ++++ b/Wrapping/Tools/vtkWrapPythonType.c +@@ -709,7 +709,7 @@ void vtkWrapPython_GenerateSpecialType( + " sizeof(PyVTKSpecialObject), // tp_basicsize\n" + " 0, // tp_itemsize\n" + " Py%s_Delete, // tp_dealloc\n" +- " nullptr, // tp_print\n" ++ " 0, // tp_vectorcall_offset\n" + " nullptr, // tp_getattr\n" + " nullptr, // tp_setattr\n" + " nullptr, // tp_compare\n" +-- +2.24.1 + diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..cf0cfcf3206 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,47 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this at non-interactive job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.2'), + ('h5py', '2.10.0', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..4846a904a7c --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,47 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this at non-interactive job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.2'), + ('h5py', '2.10.0', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From c6aa6ba511456e354acff89b210753f15c910d43 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 29 Apr 2020 15:12:46 +0200 Subject: [PATCH 284/431] fixed library endings in HDF-EOS-2.20-GCCcore-7.3.0.eb --- easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb index f75fec3c148..ea66b92df10 100644 --- a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-7.3.0.eb @@ -33,7 +33,7 @@ preconfigopts = 'export CC="$EBROOTHDF/bin/h4cc -Df2cFortran" && ' configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" sanity_check_paths = { - 'files': ['include/HdfEosDef.h', 'include/HDFEOSVersion.h', 'lib/libGctp.la', 'lib/libhdfeos.la'], + 'files': ['include/HdfEosDef.h', 'include/HDFEOSVersion.h', 'lib/libGctp.a', 'lib/libhdfeos.a'], 'dirs': ['include', 'lib'], } From c7571099ba85e24fd4d6c8f1a3e0c9d47a154d21 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 29 Apr 2020 15:15:12 +0200 Subject: [PATCH 285/431] fixed lirary endings in HDF-EOS5-1.16-foss-2018b.eb --- easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb index 63ab642efd2..e90a1ce280c 100644 --- a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-foss-2018b.eb @@ -29,7 +29,7 @@ preconfigopts = 'export CC="$EBROOTHDF5/bin/h5pcc -Df2cFortran" && ' configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" sanity_check_paths = { - 'files': ['include/HE5_HdfEosDef.h', 'include/HE5_GctpFunc.h', 'lib/libGctp.la', 'lib/libhe5_hdfeos.la'], + 'files': ['include/HE5_HdfEosDef.h', 'include/HE5_GctpFunc.h', 'lib/libGctp.a', 'lib/libhe5_hdfeos.a'], 'dirs': ['include', 'lib'], } From 55e74c29c8dcf2783b9516309e5453ea3b119e40 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Wed, 29 Apr 2020 19:25:00 +0200 Subject: [PATCH 286/431] Add Python 2 builddep for OpenPGM --- easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb index 638e978e631..a450b8ad589 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb @@ -24,6 +24,7 @@ checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] builddependencies = [ ('binutils', '2.31.1'), + ('Python', '2.7.15'), ] start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.3.0.eb index c541f21660e..7e7e5db9c5e 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.3.0.eb @@ -24,6 +24,7 @@ checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] builddependencies = [ ('binutils', '2.32'), + ('Python', '2.7.16'), ] start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb index 4640d2c70a8..7182e95bbe1 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-9.3.0.eb @@ -24,6 +24,7 @@ checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] builddependencies = [ ('binutils', '2.34'), + ('Python', '2.7.18'), ] start_dir = 'pgm' From 1a7deca3d0f1e0a219156ebc2f7fc7b9d2152f9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 19:49:01 +0200 Subject: [PATCH 287/431] add missing Python + SciPy-bundle dependendy for PETSc 3.12.4 + disable broken --with-mpi4py configure option --- ...ss-2020a.eb => PETSc-3.12.4-foss-2020a-Python-3.8.2.eb} | 7 ++++++- ...l-2020a.eb => PETSc-3.12.4-intel-2020a-Python-3.8.2.eb} | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.12.4-foss-2020a.eb => PETSc-3.12.4-foss-2020a-Python-3.8.2.eb} (83%) rename easybuild/easyconfigs/p/PETSc/{PETSc-3.12.4-intel-2020a.eb => PETSc-3.12.4-intel-2020a-Python-3.8.2.eb} (83%) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb similarity index 83% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb index 3b8adbd8656..fdba07a174e 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb @@ -1,5 +1,6 @@ name = 'PETSc' version = '3.12.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -25,6 +26,8 @@ checksums = [ builddependencies = [('CMake', '3.16.4')] dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), ('Boost', '1.72.0'), ('METIS', '5.1.0'), ('SCOTCH', '6.0.9'), @@ -33,7 +36,9 @@ dependencies = [ ('Hypre', '2.18.2'), ] -configopts = '--LIBS="$LIBS -lrt" ' +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0' shared_libs = 1 diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb similarity index 83% rename from easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb rename to easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb index 66e28a557cc..8cd4b13ee72 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb @@ -1,5 +1,6 @@ name = 'PETSc' version = '3.12.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mcs.anl.gov/petsc' description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the @@ -25,6 +26,8 @@ checksums = [ builddependencies = [('CMake', '3.16.4')] dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), ('Boost', '1.72.0'), ('METIS', '5.1.0'), ('SCOTCH', '6.0.9'), @@ -33,7 +36,9 @@ dependencies = [ ('Hypre', '2.18.2'), ] -configopts = '--LIBS="$LIBS -lrt" ' +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0' shared_libs = 1 From 3895525b67ddcd7fc129ab1db47128b3033d498c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 29 Apr 2020 16:15:30 +0200 Subject: [PATCH 288/431] reorder R6, statmod and rematch2 in R-4.0.0-foss-2020a.eb --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 1d5441ece39..fe6c733e5d6 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -325,6 +325,9 @@ exts_list = [ ('tripack', '1.3-9', { 'checksums': ['2b40670c23894b12e86a36fb2f42cab4728c8af8bd5338e94fbf86b7916a8c10'], }), + ('R6', '2.4.1', { + 'checksums': ['26b0fd64827655c28c903f7ff623e839447387f3ad9b04939a02f41ac82faa3e'], + }), ('irace', '3.4.1', { 'checksums': ['7eea92ba42e6ba320fa8bdca3c53091ae42f26a0f097244f65e7e117f6d514b6'], }), @@ -370,9 +373,6 @@ exts_list = [ ('labeling', '0.3', { 'checksums': ['0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f'], }), - ('R6', '2.4.1', { - 'checksums': ['26b0fd64827655c28c903f7ff623e839447387f3ad9b04939a02f41ac82faa3e'], - }), ('viridisLite', '0.3.0', { 'checksums': ['780ea12e7c4024d5ba9029f3a107321c74b8d6d9165262f6e64b79e00aa0c2af'], }), @@ -583,6 +583,9 @@ exts_list = [ ('boot', '1.3-25', { 'checksums': ['464835fcb453072346ce49e4ae318e04c9dba682349be49db616623b6088fbbe'], }), + ('statmod', '1.4.34', { + 'checksums': ['1a81c286e099d2395e39f47f1e87295b8e1d64b64ec55bb09bc817ae8879747a'], + }), ('lme4', '1.1-23', { 'checksums': ['99d542b1f78fae33a64f1b8eec33b7a4532a8d82d2ac47bdb2838248f14c0262'], }), @@ -1159,9 +1162,6 @@ exts_list = [ ('ipred', '0.9-9', { 'checksums': ['0da87a70730d5a60b97e46b2421088765e7d6a7cc2695757eba0f9d31d86416f'], }), - ('statmod', '1.4.34', { - 'checksums': ['1a81c286e099d2395e39f47f1e87295b8e1d64b64ec55bb09bc817ae8879747a'], - }), ('miscTools', '0.6-26', { 'checksums': ['be3c5a63ca12ce7ce4d43767a1815cd3dcf32664728ade251cfb03ea6f77fc9a'], }), @@ -1489,6 +1489,9 @@ exts_list = [ ('gh', '1.1.0', { 'checksums': ['de9faf383c3fe5e87a75391d82cf71b1331b3c80cd00c4203146a303825d89ad'], }), + ('rematch2', '2.1.1', { + 'checksums': ['d0423a418e8b46ac3a4819af7a7d19c39ca7c8c862c1e9a1c1294aa19152518f'], + }), ('usethis', '1.6.1', { 'checksums': ['60339059a97ed07dea7f8908b828b5bb42e0fd0b471165c061bc9660b0d59d6f'], }), @@ -2146,9 +2149,6 @@ exts_list = [ ('GenSA', '1.1.7', { 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], }), - ('rematch2', '2.1.1', { - 'checksums': ['d0423a418e8b46ac3a4819af7a7d19c39ca7c8c862c1e9a1c1294aa19152518f'], - }), ('parsedate', '1.2.0', { 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], }), From f6e5295306fa9a46ae41e27bdbac85ebe5e048d7 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Wed, 29 Apr 2020 21:46:57 +0200 Subject: [PATCH 289/431] Fix OpenPGM url --- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb index a450b8ad589..2b9c2f2a97a 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'OpenPGM' version = '5.2.122' -homepage = 'http://code.google.com/p/openpgm/' +homepage = 'https://code.google.com/p/openpgm/' description = """ OpenPGM is an open source implementation of the Pragmatic General Multicast From 501d788f64a77dcae3020c5c03b92fe2727d2018 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 29 Apr 2020 22:48:42 +0200 Subject: [PATCH 290/431] Added ibverbs dependencies. Requires https://github.com/easybuilders/easybuild-framework/pull/3309 --- .../p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb | 2 ++ .../p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb index 8e5a2aa71ae..93fb43172fe 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb @@ -16,6 +16,8 @@ local_mkdir_and_extract_cmd_pattern = "DIR=%s/%s; mkdir -p $DIR; tar -C $DIR --s source_urls = ['https://github.com/pytorch/pytorch/archive'] +osdependencies = [OSPACKAGES_IBVERBS] + # PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. # determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.4.0/third_party sources = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb index f936e160c26..c496e380a34 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb @@ -16,6 +16,8 @@ local_mkdir_and_extract_cmd_pattern = "DIR=%s/%s; mkdir -p $DIR; tar -C $DIR --s source_urls = ['https://github.com/pytorch/pytorch/archive'] +osdependencies = [OSPACKAGES_IBVERBS] + # PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. # determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.4.0/third_party sources = [ From 83c08b2abff3d1a1d138e6dbe2e975d04bb9d3a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 08:13:50 +0200 Subject: [PATCH 291/431] add missing ROI, Rglpk, ROI.plugin.glpk extensions in R 4.0.0 easyconfig --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index fe6c733e5d6..344c8d6414a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -1885,6 +1885,15 @@ exts_list = [ ('gmp', '0.5-13.6', { 'checksums': ['39a61618cc9eeabd00665cc5f24721e75f0dec8268059a0d18c907c2adf85a48'], }), + ('ROI', '0.3-3', { + 'checksums': ['2977604b9def46a3638d56a7efa890f2e84fa320bece693d03c196771466a919'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '0.3-0', { + 'checksums': ['160ac14d20c217ff186912c06d53bccf2a33664977ae4c6fc5113a7ac8533ba8'], + }), ('spaMM', '3.2.0', { 'checksums': ['40d54ad52c4839f33baa1e488e1e76042e57083ff7780f9c5640c49340ff2999'], }), From 550b60351dcee0b883984759cf9ec72ac169f033 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 08:34:41 +0200 Subject: [PATCH 292/431] add GLPK as dep for R 4.0.0 (required for Rglpk) --- .../g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb | 30 +++++++++++++++++++ .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 1 + 2 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..7b7baf4981b --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-9.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.65' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4281e29b628864dfe48d393a7bedd781e5b475387c20d8b0158f329994721a10'] + +builddependencies = [('binutils', '2.34')] +dependencies = [('GMP', '6.2.0')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 344c8d6414a..a0cb9a693fd 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -42,6 +42,7 @@ dependencies = [ ('UDUNITS', '2.2.26'), # for units ('GSL', '2.6'), # for RcppGSL ('ImageMagick', '7.0.10-1'), # for animation + ('GLPK', '4.65'), # for Rglpk # OS dependency should be preferred if the os version is more recent then # this version, it's nice to have an up to date openssl for security # reasons From b5ed28bc34523ffe28eabfa0d0672791a13faaa5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 08:51:39 +0200 Subject: [PATCH 293/431] add qgam dep for DHARMa in R 4.0.0 easyconfig --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index a0cb9a693fd..c38960af58c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -1898,6 +1898,9 @@ exts_list = [ ('spaMM', '3.2.0', { 'checksums': ['40d54ad52c4839f33baa1e488e1e76042e57083ff7780f9c5640c49340ff2999'], }), + ('qgam', '1.3.2', { + 'checksums': ['273a40d0bfdc340c049bcb85aea83acd887868d8a69c0062b8399e0b24137a52'], + }), ('DHARMa', '0.3.0', { 'checksums': ['1c7ac2f1897ca62e0ebb7367c4b31866515c8503d0fa645fa5e8ac5172310298'], }), From 01347e868f1b6d0ea779e8325ab2f31d5ed1fb7e Mon Sep 17 00:00:00 2001 From: Tardi Gradus Date: Thu, 30 Apr 2020 09:39:57 +0200 Subject: [PATCH 294/431] Update easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb Add extra paths to sanity_check_paths Co-Authored-By: Alex Domingo --- easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb index 74154508346..c4b44a65e36 100644 --- a/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb +++ b/easybuild/easyconfigs/g/gretl/gretl-2020a-foss-2019a.eb @@ -34,8 +34,8 @@ preconfigopts = 'export LDFLAGS="-fopenmp $LDFLAGS" && ' configopts = '--disable-json ' sanity_check_paths = { - 'files': ['bin/gretl', 'bin/gretlcli'], - 'dirs': ['bin', 'share'] + 'files': ['bin/gretl', 'bin/gretlcli', 'bin/gretlmpi', 'lib/libgretl-1.0.%s' % SHLIB_EXT], + 'dirs': ['include/gretl', 'share'] } moduleclass = 'math' From b0caf6b4c0f57e4220868772cdc702ab4f9c502e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 10:34:58 +0200 Subject: [PATCH 295/431] add missing Bison build dep in Graphviz easyconfigs --- .../g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb | 2 +- easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb | 2 ++ .../g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb | 2 +- 5 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb index 1fa01aea1eb..59d35995886 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb @@ -38,7 +38,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ('Autotools', '20180311'), ('flex', '2.6.4'), - ('libtool', '2.4.6'), + ('Bison', '3.0.5'), ('SWIG', '3.0.12', versionsuffix), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb index 6199ac03a4b..3021e525001 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb @@ -36,7 +36,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ('Autotools', '20180311'), ('flex', '2.6.4'), - ('libtool', '2.4.6'), + ('Bison', '3.0.5'), ('SWIG', '3.0.12', '-Python-3.6.6'), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb index 96d633dc83e..c8a44093c8a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb @@ -46,6 +46,8 @@ dependencies = [ builddependencies = [ ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), ('SWIG', '3.0.12', '-Python-3.6.4'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb index 65900e3b4f7..1ca2e2d4744 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb @@ -33,7 +33,7 @@ checksums = [ builddependencies = [ ('Autotools', '20180311'), ('flex', '2.6.4'), - ('libtool', '2.4.6'), + ('Bison', '3.3.2'), ('SWIG', '4.0.1'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb index 6baf6a62db4..def5b531355 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb @@ -28,7 +28,7 @@ checksums = [ builddependencies = [ ('Autotools', '20180311'), ('flex', '2.6.4'), - ('libtool', '2.4.6'), + ('Bison', '3.3.2'), ('SWIG', '4.0.1'), ('pkg-config', '0.29.2'), ] From 3e0acb849e62e0ff62028152954c2dcb3031e7f8 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 30 Apr 2020 11:42:33 +0200 Subject: [PATCH 296/431] adding easyconfigs: Arlequin-3.5.2.2-foss-2019b.eb --- .../a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb diff --git a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb new file mode 100644 index 00000000000..f26592aec88 --- /dev/null +++ b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb @@ -0,0 +1,91 @@ +easyblock = 'Bundle' + +name = 'Arlequin' +version = '3.5.2.2' + +# HTTPS not working +homepage = 'http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html' +description = "Arlequin: An Integrated Software for Population Genetics Data Analysis" + +toolchain = {'name': 'foss', 'version': '2019b'} + +default_component_specs = { + 'source_urls': ['http://cmpg.unibe.ch/software/arlequin35/linux/'], +} + +components = [ + ('arlecore', version, { + 'easyblock': 'Tarball', + 'sources': [ + { + 'download_filename': '%(name)s_linux.zip', + 'filename': '%(name)s-%(version)s.zip', + }, + ], + 'patches': ['%(name)s-%(version)s_fix-bash.patch'], + 'checksums': [ + '79d7ce0c126c32f88a66290aabd29e0b2e5b2d8c46cbcf02ef95ac7cbb91ead8', # arlecore_linux-3.5.2.2.zip + '5943db21213509ee06e0a32f7f80790313bf72f0243246c9a579b35be519974c', # arlecore-3.5.2.2_fix-bash.patch + ], + }), + ('arlsumstat', version, { + 'easyblock': 'PackedBinary', + 'sources': [ + { + 'download_filename': '%(name)s_linux.zip', + 'filename': '%(name)s-%(version)s.zip', + }, + ], + 'patches': ['%(name)s-%(version)s_fix-bash.patch'], + 'checksums': [ + '709590b42d1ad5060cce4d90debe4ef2b9c0d1986f3d8dffd80c7b694d0ff454', # arlsumstat_linux-3.5.2.2.zip + '3584208bb1756312340ecdf2dfe04f67696b20ab17d6872d6c11a53cb4089d8b', # arlsumstat-3.5.2.2_fix-bash.patch + ], + }), + ('arlequin_examples', version, { + 'easyblock': 'Tarball', + 'sources': [ + { + 'download_filename': 'Example%20files_linux.zip', + 'filename': '%(name)s-%(version)s.zip', + }, + ], + 'checksums': [ + '58e76d888ff2f4631df2ac482dd1e3c44cda389f9c31f7512993a852610cd985', # Example%20files_linux-3.5.2.2.zip + ], + }), +] + +local_arlecore_bin = 'arlecore_linux/arlecore3522_64bit' +local_arlecore_sh = 'arlecore_linux/LaunchArlecore.sh' +local_arlsumstat_bin = 'arlsumstat_linux/arlsumstat3522_64bit' +local_arlsumstat_sh = 'arlsumstat_linux/LaunchArlSumStat.sh' + +postinstallcmds = [ + # fix arlecore + 'sed -i "s@^arlecore=.*@arlecore=%%(installdir)s/%s@g" %%(installdir)s/%s' + % (local_arlecore_bin, local_arlecore_sh), + 'chmod +x %%(installdir)s/%s' % local_arlecore_bin, + 'chmod +x %%(installdir)s/%s' % local_arlecore_sh, + # fix arlsumstat + 'sed -i "s@^arlsumstat=.*@arlsumstat=%%(installdir)s/%s@g" %%(installdir)s/%s' + % (local_arlsumstat_bin, local_arlsumstat_sh), + 'chmod +x %%(installdir)s/%s' % local_arlsumstat_bin, + 'chmod +x %%(installdir)s/%s' % local_arlsumstat_sh, +] +dependencies = [ + ('R', '3.6.2'), +] + +modextrapaths = {'PATH': ['arlecore_linux', 'arlsumstat_linux']} + +sanity_check_paths = { + 'files': [local_arlecore_bin, local_arlecore_sh, local_arlsumstat_bin, local_arlsumstat_sh], + 'dirs': [], +} + +sanity_check_commands = [ + 'LaunchArlecore.sh', + 'LaunchArlSumStat.sh', + r'cd %(installdir)s/Example\ files_linux/ELB/ && LaunchArlecore.sh -s "Xdata.ars"', +] From ed4676b32b079677a48b03e1c15be6ac6304c3b8 Mon Sep 17 00:00:00 2001 From: darkless Date: Thu, 30 Apr 2020 11:43:30 +0200 Subject: [PATCH 297/431] add Arlequin patch files for components --- .../Arlequin/arlecore-3.5.2.2_fix-bash.patch | 44 +++++++++++++ .../arlsumstat-3.5.2.2_fix-bash.patch | 65 +++++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arlequin/arlecore-3.5.2.2_fix-bash.patch create mode 100644 easybuild/easyconfigs/a/Arlequin/arlsumstat-3.5.2.2_fix-bash.patch diff --git a/easybuild/easyconfigs/a/Arlequin/arlecore-3.5.2.2_fix-bash.patch b/easybuild/easyconfigs/a/Arlequin/arlecore-3.5.2.2_fix-bash.patch new file mode 100644 index 00000000000..98dfb18f276 --- /dev/null +++ b/easybuild/easyconfigs/a/Arlequin/arlecore-3.5.2.2_fix-bash.patch @@ -0,0 +1,44 @@ +Fix default binary for arlecore +Add option to specify variables via command line args + +Author: Pavel Grochal (INUITS) +diff -ru --new-file arlecore_linux.orig/LaunchArlecore.sh arlecore_linux/LaunchArlecore.sh +--- arlecore_linux.orig/LaunchArlecore.sh 2015-04-11 17:28:48.000000000 +0200 ++++ arlecore_linux/LaunchArlecore.sh 2020-04-30 10:01:49.502359866 +0200 +@@ -10,10 +10,25 @@ + # graphical interface). + + #Modify the following line to state which version of arlecore you are using +-arlecore=arlecore64.exe #windows version ++arlecore=arlecore3522_64bit #Linux version + #Modify this if you wan to use another setting file + settingsFile=arl_run.ars + ++#Easybuild fix ++while getopts ":b:s:" opt; do ++ case $opt in ++ b) arlecore="$OPTARG" ++ ;; ++ s) settingsFile="$OPTARG" ++ ;; ++ \?) echo "Invalid option -$OPTARG ++Use -b to specify path to arlecore binary. ++Use -s to specify settings file." >&2 ++ exit 1 ++ ;; ++ esac ++done ++ + if [ -f $settingsFile ]; then + + #This loop will analyse all files with the same settings file +@@ -21,7 +36,7 @@ + do + echo "Processing file $file" + #Launch arlecore with the same settings for all files +- ./$arlecore $file $settingsFile run_silent ++ $arlecore $file $settingsFile run_silent + done + + #The following loop would be an alternative to perform specific computations on each file +Binary files arlecore_linux.orig/.Makefile.swp and arlecore_linux/.Makefile.swp differ diff --git a/easybuild/easyconfigs/a/Arlequin/arlsumstat-3.5.2.2_fix-bash.patch b/easybuild/easyconfigs/a/Arlequin/arlsumstat-3.5.2.2_fix-bash.patch new file mode 100644 index 00000000000..0223df015b3 --- /dev/null +++ b/easybuild/easyconfigs/a/Arlequin/arlsumstat-3.5.2.2_fix-bash.patch @@ -0,0 +1,65 @@ +Fix default binary for arlsumstat +Add option to specify variables via command line args + +Author: Pavel Grochal (INUITS) +diff -ru --new-file arlsumstat_linux.orig/LaunchArlSumStat.sh arlsumstat_linux/LaunchArlSumStat.sh +--- arlsumstat_linux.orig/LaunchArlSumStat.sh 2015-04-11 17:30:24.000000000 +0200 ++++ arlsumstat_linux/LaunchArlSumStat.sh 2020-04-30 10:02:09.806949125 +0200 +@@ -10,7 +10,7 @@ + # graphical interface). + + #Modify the following line to state which version of arlsumstat you are using +-arlsumstat=arlsumstat64.exe #Windows version ++arlsumstat=arlsumstat3522_64bit #Linux version + #Modify the follwing name to specify the name of the output file for the summary statistics + outss=outSumStats.txt + +@@ -19,6 +19,28 @@ + + #Change the following line if you want to use another settings file for the computations + settingsFile=arl_run.ars ++ ++#Easybuild fix ++while getopts ":b:f:o:s:" opt; do ++ case $opt in ++ b) arlsumstat="$OPTARG" ++ ;; ++ f) fileList="$OPTARG" ++ ;; ++ o) outss="$OPTARG" ++ ;; ++ s) settingsFile="$OPTARG" ++ ;; ++ \?) echo "Invalid option -$OPTARG ++Use -b to specify path to arlsumstat binary. ++Use -f to specify project files list. ++Use -o to specify output file for the summary statistics. ++Use -s to specify settings file." >&2 ++ exit 1 ++ ;; ++ esac ++done ++ + if [ "$settingsFile" != "arl_run.ars" ]; then + if [ -f $settingsFile ]; then + echo "copying file $settingsFile to arl_run.ars" +@@ -32,12 +54,12 @@ + counter=1; + for file in *.arp + do +- if [ $counter -eq 1 ]; then ++ if [ $counter -eq 1 ]; then + #Reset file list + (echo "$counter $file") > $fileList + echo "Processing file $file" + #Compute stats, reset output file and include header +- ./$arlsumstat ./$file $outss 0 1 run_silent ++ $arlsumstat ./$file $outss 0 1 run_silent + else + #Append file list + (echo "$counter $file") >> $fileList +@@ -50,4 +72,3 @@ + rm ${file%.*}.res -r + let counter=counter+1 + done +- From 16b9a2b98751aa83edcb4b98ef09b63637c16e77 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 30 Apr 2020 11:55:35 +0200 Subject: [PATCH 298/431] push Alpha to commit 3139d8186403 --- ...6.eb => Alpha-20200430-foss-2019b-Python-2.7.16.eb} | 10 +++++----- ..._fix-email.patch => Alpha-20200430_fix-email.patch} | 0 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/a/Alpha/{Alpha-20190607-foss-2019b-Python-2.7.16.eb => Alpha-20200430-foss-2019b-Python-2.7.16.eb} (91%) rename easybuild/easyconfigs/a/Alpha/{Alpha-20190607_fix-email.patch => Alpha-20200430_fix-email.patch} (100%) diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb similarity index 91% rename from easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb rename to easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb index afa0812925f..05bee948667 100644 --- a/easybuild/easyconfigs/a/Alpha/Alpha-20190607-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/a/Alpha/Alpha-20200430-foss-2019b-Python-2.7.16.eb @@ -1,8 +1,8 @@ easyblock = 'Bundle' name = 'Alpha' -version = '20190607' -local_alpha_commit = 'e027eb0fea1e' +version = '20200430' +local_alpha_commit = '3139d8186403' local_pyinc_commit = '0f8a00b8c10c' versionsuffix = '-Python-%(pyver)s' @@ -46,11 +46,11 @@ components = [ (name, version, { 'easyblock': 'Tarball', 'source_urls': ['https://bitbucket.org/thekswenson/%(namelower)s/get/'], - 'sources': [{'download_filename': '%s.zip' % local_alpha_commit, 'filename': '%(namelower)s-%(version)s.zip'}], + 'sources': [{'download_filename': '%s.zip' % local_alpha_commit, 'filename': '%(name)s-%(version)s.zip'}], 'patches': ['%s-%s_fix-email.patch' % (name, version)], 'checksums': [ - 'a9a0857ee080864c0d187f1f537aebdb3a61e58dd555b97dffbf2c2d73465f2a', # alpha-e027eb0fea1e.zip - '342d5d37bcfc19a2487c3b08860adc4246736919948b1968f899b0c595d7125d', # Alpha-20190607_fix-email.patch + '07a2b601305b82fce77c2eaf53c5c550f0f8dbaacd1f314433dab2053f91aaf9', # Alpha-20200430.zip + '342d5d37bcfc19a2487c3b08860adc4246736919948b1968f899b0c595d7125d', # Alpha-20200430_fix-email.patch ], 'start_dir': 'thekswenson-%%(namelower)s-%s' % local_alpha_commit, 'install_type': 'subdir', diff --git a/easybuild/easyconfigs/a/Alpha/Alpha-20190607_fix-email.patch b/easybuild/easyconfigs/a/Alpha/Alpha-20200430_fix-email.patch similarity index 100% rename from easybuild/easyconfigs/a/Alpha/Alpha-20190607_fix-email.patch rename to easybuild/easyconfigs/a/Alpha/Alpha-20200430_fix-email.patch From 5ccf46b606d4f4e061981530437cd819d968d0a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 12:13:49 +0200 Subject: [PATCH 299/431] use https:// in Graphviz homepage --- easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb index c8a44093c8a..74ba7b4c8c7 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Graphviz' version = '2.40.1' -homepage = 'http://www.graphviz.org/' +homepage = 'https://www.graphviz.org/' description = """Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, From 8ce3c451ef0f8c33dc11d3a97b5d602abece20da Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 30 Apr 2020 13:25:05 +0200 Subject: [PATCH 300/431] fixed remarks --- .../a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb | 32 ++++++++----------- 1 file changed, 13 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb index f26592aec88..db766fa0d25 100644 --- a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb +++ b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb @@ -10,18 +10,16 @@ description = "Arlequin: An Integrated Software for Population Genetics Data Ana toolchain = {'name': 'foss', 'version': '2019b'} default_component_specs = { - 'source_urls': ['http://cmpg.unibe.ch/software/arlequin35/linux/'], + 'source_urls': ['http://cmpg.unibe.ch/software/arlequin%(version_major)s%(version_minor)s/linux/'], } components = [ ('arlecore', version, { 'easyblock': 'Tarball', - 'sources': [ - { - 'download_filename': '%(name)s_linux.zip', - 'filename': '%(name)s-%(version)s.zip', - }, - ], + 'sources': [{ + 'download_filename': '%(name)s_linux.zip', + 'filename': '%(name)s-%(version)s.zip', + }], 'patches': ['%(name)s-%(version)s_fix-bash.patch'], 'checksums': [ '79d7ce0c126c32f88a66290aabd29e0b2e5b2d8c46cbcf02ef95ac7cbb91ead8', # arlecore_linux-3.5.2.2.zip @@ -30,12 +28,10 @@ components = [ }), ('arlsumstat', version, { 'easyblock': 'PackedBinary', - 'sources': [ - { - 'download_filename': '%(name)s_linux.zip', - 'filename': '%(name)s-%(version)s.zip', - }, - ], + 'sources': [{ + 'download_filename': '%(name)s_linux.zip', + 'filename': '%(name)s-%(version)s.zip', + }], 'patches': ['%(name)s-%(version)s_fix-bash.patch'], 'checksums': [ '709590b42d1ad5060cce4d90debe4ef2b9c0d1986f3d8dffd80c7b694d0ff454', # arlsumstat_linux-3.5.2.2.zip @@ -44,12 +40,10 @@ components = [ }), ('arlequin_examples', version, { 'easyblock': 'Tarball', - 'sources': [ - { - 'download_filename': 'Example%20files_linux.zip', - 'filename': '%(name)s-%(version)s.zip', - }, - ], + 'sources': [{ + 'download_filename': 'Example%20files_linux.zip', + 'filename': '%(name)s-%(version)s.zip', + }], 'checksums': [ '58e76d888ff2f4631df2ac482dd1e3c44cda389f9c31f7512993a852610cd985', # Example%20files_linux-3.5.2.2.zip ], From b33f8af3ab128dee228e5a01d3df075b8b9fcd48 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 30 Apr 2020 13:50:18 +0200 Subject: [PATCH 301/431] fixed comments --- .../easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb index db766fa0d25..88ef6fff349 100644 --- a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb +++ b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb @@ -22,7 +22,7 @@ components = [ }], 'patches': ['%(name)s-%(version)s_fix-bash.patch'], 'checksums': [ - '79d7ce0c126c32f88a66290aabd29e0b2e5b2d8c46cbcf02ef95ac7cbb91ead8', # arlecore_linux-3.5.2.2.zip + '79d7ce0c126c32f88a66290aabd29e0b2e5b2d8c46cbcf02ef95ac7cbb91ead8', # arlecore-3.5.2.2.zip '5943db21213509ee06e0a32f7f80790313bf72f0243246c9a579b35be519974c', # arlecore-3.5.2.2_fix-bash.patch ], }), @@ -34,7 +34,7 @@ components = [ }], 'patches': ['%(name)s-%(version)s_fix-bash.patch'], 'checksums': [ - '709590b42d1ad5060cce4d90debe4ef2b9c0d1986f3d8dffd80c7b694d0ff454', # arlsumstat_linux-3.5.2.2.zip + '709590b42d1ad5060cce4d90debe4ef2b9c0d1986f3d8dffd80c7b694d0ff454', # arlsumstat-3.5.2.2.zip '3584208bb1756312340ecdf2dfe04f67696b20ab17d6872d6c11a53cb4089d8b', # arlsumstat-3.5.2.2_fix-bash.patch ], }), @@ -44,9 +44,7 @@ components = [ 'download_filename': 'Example%20files_linux.zip', 'filename': '%(name)s-%(version)s.zip', }], - 'checksums': [ - '58e76d888ff2f4631df2ac482dd1e3c44cda389f9c31f7512993a852610cd985', # Example%20files_linux-3.5.2.2.zip - ], + 'checksums': ['58e76d888ff2f4631df2ac482dd1e3c44cda389f9c31f7512993a852610cd985'], }), ] From 1ccfa7194ac8453eae6aa719db913497a642cb61 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 17:05:28 +0200 Subject: [PATCH 302/431] adding easyconfigs: CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb, UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb, python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb --- ...seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb | 52 +++++++++++++++++++ ...enshtein-0.12.0-foss-2019b-Python-3.7.4.eb | 27 ++++++++++ ...UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb | 39 ++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..9305c8fb5eb --- /dev/null +++ b/easybuild/easyconfigs/c/CITE-seq-Count/CITE-seq-Count-1.4.3-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'CITE-seq-Count' +version = '1.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Hoohm/CITE-seq-Count' +description = "A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment." + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('UMI-tools', '1.0.1', versionsuffix), + ('python-Levenshtein', '0.12.0', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('pytest-dependency', '0.5.1', { + 'checksums': ['c2a892906192663f85030a6ab91304e508e546cddfe557d692d61ec57a1d946b'], + }), + ('pybktree', '1.1', { + 'checksums': ['eec0037cdd3d7553e6d72435a4379bede64be17c6712f149e485169638154d2b'], + }), + ('dill', '0.3.1.1', { + 'checksums': ['42d8ef819367516592a825746a18073ced42ca169ab1f5f4044134703e7a049c'], + }), + ('multiprocess', '0.70.9', { + 'checksums': ['9fd5bd990132da77e73dec6e9613408602a4612e1d73caf2e2b813d2b61508e5'], + }), + (name, version, { + 'modulename': 'cite_seq_count', + 'checksums': ['bf046339eb0e587114134e1f0300f027a56f361de3a38839f5d7a436b4a595bc'], + # remove (too) strict version pinning for dependencies + 'preinstallopts': "sed -i'' 's/==/>=/g' setup.py && " + }), +] + +sanity_check_paths = { + 'files': ['bin/CITE-seq-Count'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["CITE-seq-Count --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..2200977a737 --- /dev/null +++ b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'python-Levenshtein' +version = '0.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.org/project/python-Levenshtein/' +description = 'Python extension for computing string edit distances and similarities.' + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['033a11de5e3d19ea25c9302d11224e1a1898fe5abd23c61c7c360c25195e3eb1'] + +dependencies = [ + ('Python', '3.7.4'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'Levenshtein'} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..de8ea9fac13 --- /dev/null +++ b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.0.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'UMI-tools' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://umi-tools.readthedocs.io' +description = "Tools for handling Unique Molecular Identifiers in NGS data sets" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('matplotlib', '3.1.1', versionsuffix), + ('Pysam', '0.15.3'), +] + +use_pip = True + +exts_list = [ + ('regex', '2020.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['295badf61a51add2d428a46b8580309c520d8b26e769868b922750cf3ce67142'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/CGATOxford/UMI-tools/archive/'], + 'checksums': ['f27e23d6c51f97239547d7093ddb5c039d0e13301e25cc4b1c568b9029e20649'], + }), +] + +sanity_check_paths = { + 'files': ['bin/umi_tools'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 448f64b2e44b24142d18c686e39c5aca45777319 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 30 Apr 2020 17:31:31 +0200 Subject: [PATCH 303/431] adding easyconfigs: MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb, MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb --- ...Analysis-0.20.1-foss-2019b-Python-3.7.4.eb | 49 +++++++++++++++++++ ...nalysis-0.20.1-intel-2019b-Python-3.7.4.eb | 49 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..50dbfd6d731 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '0.20.1' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('networkx', '2.4', versionsuffix), +] + +exts_default_options = { + 'download_dep_fail': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('GridDataFormats', '0.4.0', { + 'modulename': 'gridData', + 'checksums': ['f81d6b75aa7ebd9e8b64e14558c2d2583a0589829382beb4ef69860110261512'], + }), + ('gsd', '2.1.1', { + 'checksums': ['9c0571761231057df6eb3d5e170df0cb81750a057f7c4685608a4bcd382028fa'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..6de6ae4e66e --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '0.20.1' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('networkx', '2.4', versionsuffix), +] + +exts_default_options = { + 'download_dep_fail': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('GridDataFormats', '0.4.0', { + 'modulename': 'gridData', + 'checksums': ['f81d6b75aa7ebd9e8b64e14558c2d2583a0589829382beb4ef69860110261512'], + }), + ('gsd', '2.1.1', { + 'checksums': ['9c0571761231057df6eb3d5e170df0cb81750a057f7c4685608a4bcd382028fa'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['d04b71b193b9716d2597ffb9938b93f43487fa535da1bb5c1f2baccf356d7df9'], + }), +] + +moduleclass = 'bio' From e120d691909a9e7c7a71bec83427226d52b90fd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 18:06:48 +0200 Subject: [PATCH 304/431] add MCE::Mutex extension to Perl 5.28.1 + 5.30.x --- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 5 +++++ 3 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index 1317e5f79a7..b9573dbb48d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -1740,6 +1740,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], }), + ('MCE::Mutex', '1.866', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/'], + 'checksums': ['087ad6d6a495d823771e5bc23bcbcd31c683289b5cb45fc4e857449f9ea7aa1b'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb index 3a92847cd5e..7692b7a48d1 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb @@ -1737,6 +1737,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], }), + ('MCE::Mutex', '1.866', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/'], + 'checksums': ['087ad6d6a495d823771e5bc23bcbcd31c683289b5cb45fc4e857449f9ea7aa1b'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index 8a0d98ae4a8..8b6edb3963a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -1717,6 +1717,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], }), + ('MCE::Mutex', '1.866', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/'], + 'checksums': ['087ad6d6a495d823771e5bc23bcbcd31c683289b5cb45fc4e857449f9ea7aa1b'], + }), ] moduleclass = 'lang' From d68e1993026cce2f1c38d2c8174dbfeb7e49dc07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 18:19:06 +0200 Subject: [PATCH 305/431] adding easyconfigs: cdbfasta-0.99-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb --- ...99-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..04682d19781 --- /dev/null +++ b/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'cdbfasta' +version = '0.99' + +homepage = 'https://sourceforge.net/projects/cdbfasta' +description = "Fasta file indexing and retrival tool" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +builddependencies = [ + ('zlib', '1.2.11'), +] + +prebuildopts = "sed -i'' 's/DENABLE_COMPRESSION=0/DENABLE_COMPRESSION=1/g' Makefile && unset LIBS && " +buildopts = 'ZDIR="$EBROOTZLIB" CC="$CXX" DBGFLAGS="$CXXFLAGS" LINKER="$CXX $CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From 466ada3730d451af55c31d4615339afa8b92f26b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 18:19:30 +0200 Subject: [PATCH 306/431] adding easyconfigs: cdbfasta-0.99-GCC-8.3.0.eb --- .../c/cdbfasta/cdbfasta-0.99-GCC-8.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-GCC-8.3.0.eb b/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-GCC-8.3.0.eb new file mode 100644 index 00000000000..0248913c5ef --- /dev/null +++ b/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-GCC-8.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'cdbfasta' +version = '0.99' + +homepage = 'https://sourceforge.net/projects/cdbfasta' +description = "Fasta file indexing and retrival tool" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +builddependencies = [ + ('zlib', '1.2.11'), +] + +prebuildopts = "sed -i'' 's/DENABLE_COMPRESSION=0/DENABLE_COMPRESSION=1/g' Makefile && unset LIBS && " +buildopts = 'ZDIR="$EBROOTZLIB" CC="$CXX" DBGFLAGS="$CXXFLAGS" LINKER="$CXX $CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From d71e7c64bf5a7abb40dbac2dced5119a24355535 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 30 Apr 2020 18:35:28 +0200 Subject: [PATCH 307/431] Put some parameters into global scope --- .../MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb | 7 ++++--- .../MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb index 50dbfd6d731..57c7ba4dbb2 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb @@ -18,11 +18,12 @@ dependencies = [ ('networkx', '2.4', versionsuffix), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + exts_default_options = { - 'download_dep_fail': True, 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'sanity_pip_check': True, } exts_list = [ diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb index 6de6ae4e66e..a4168d99e79 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb @@ -18,11 +18,12 @@ dependencies = [ ('networkx', '2.4', versionsuffix), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + exts_default_options = { - 'download_dep_fail': True, 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'sanity_pip_check': True, } exts_list = [ From 1190b7cfca0dff5f84d6026145ce087116133652 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 19:25:12 +0200 Subject: [PATCH 308/431] add easyconfig for cdbfasta 0.99 w/ iccifort/2019.5.281 --- .../cdbfasta-0.99-iccifort-2019.5.281.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.5.281.eb b/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..b63395f79c5 --- /dev/null +++ b/easybuild/easyconfigs/c/cdbfasta/cdbfasta-0.99-iccifort-2019.5.281.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'cdbfasta' +version = '0.99' + +homepage = 'https://sourceforge.net/projects/cdbfasta' +description = "Fasta file indexing and retrival tool" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +builddependencies = [ + ('zlib', '1.2.11'), +] + +prebuildopts = "sed -i'' 's/DENABLE_COMPRESSION=0/DENABLE_COMPRESSION=1/g' Makefile && unset LIBS && " +buildopts = 'ZDIR="$EBROOTZLIB" CC="$CXX" DBGFLAGS="$CXXFLAGS" LINKER="$CXX $CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From 93cd465fa075776cc35361d20fa4e2ae53807911 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 19:26:56 +0200 Subject: [PATCH 309/431] adding easyconfigs: ProtHint-2.4.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1-Python-3.7.2.eb --- ...019.1.144-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1-Python-3.7.2.eb new file mode 100644 index 00000000000..649f8041b54 --- /dev/null +++ b/easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -0,0 +1,46 @@ +easyblock = 'Tarball' + +name = 'ProtHint' +version = '2.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gatech-genemark/ProtHint' +description = """ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and + stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of + reference protein sequences.""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = ['https://github.com/gatech-genemark/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['bcdba61ff1624e2af46497b68bfac89690c295f09a59841e3faa90b6be4eef98'] + +dependencies = [ + ('Perl', '5.28.1'), + ('Python', '3.7.2'), + ('GeneMark-ET', '4.38'), + ('DIAMOND', '0.9.24'), + ('spaln', '2.3.3c'), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/prothint.py'], + 'dirs': [], +} + +# see https://github.com/gatech-genemark/ProtHint/tree/master/example +local_test_cmd = "cp -a %(installdir)s/example %(builddir)s && cd %(builddir)s/example/input && " +local_test_cmd += "prothint.py genome.fasta proteins.fasta --geneMarkGtf genemark.gtf --workdir ../test && " +# verify results using recursive 'diff', which exists with non-zero exit code if a difference was found +local_test_cmd += "cd %(builddir)s/example && " +local_test_cmd += "diff -ru <(sort output/prothint.gff) <(sort test/prothint.gff) && " +local_test_cmd += "diff -ru <(sort output/evidence.gff) <(sort test/evidence.gff)" + +sanity_check_commands = [ + "prothint.py --help", + local_test_cmd, +] + +moduleclass = 'bio' From a3dd215d9aba200bc929695bf030385be1a2e8ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 21:26:14 +0200 Subject: [PATCH 310/431] add easyconfig for ProtHint 2.4.0 with iccifort/2019.5.281 --- ...-2.4.0-iccifort-2019.5.281-Python-3.7.4.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.5.281-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.5.281-Python-3.7.4.eb b/easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.5.281-Python-3.7.4.eb new file mode 100644 index 00000000000..1644151b0f7 --- /dev/null +++ b/easybuild/easyconfigs/p/ProtHint/ProtHint-2.4.0-iccifort-2019.5.281-Python-3.7.4.eb @@ -0,0 +1,46 @@ +easyblock = 'Tarball' + +name = 'ProtHint' +version = '2.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gatech-genemark/ProtHint' +description = """ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and + stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of + reference protein sequences.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://github.com/gatech-genemark/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['bcdba61ff1624e2af46497b68bfac89690c295f09a59841e3faa90b6be4eef98'] + +dependencies = [ + ('Perl', '5.30.0'), + ('Python', '3.7.4'), + ('GeneMark-ET', '4.57'), + ('DIAMOND', '0.9.30'), + ('spaln', '2.4.03'), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/prothint.py'], + 'dirs': [], +} + +# see https://github.com/gatech-genemark/ProtHint/tree/master/example +local_test_cmd = "cp -a %(installdir)s/example %(builddir)s && cd %(builddir)s/example/input && " +local_test_cmd += "prothint.py genome.fasta proteins.fasta --geneMarkGtf genemark.gtf --workdir ../test && " +# verify results using recursive 'diff', which exists with non-zero exit code if a difference was found +local_test_cmd += "cd %(builddir)s/example && " +local_test_cmd += "diff -ru <(sort output/prothint.gff) <(sort test/prothint.gff) && " +local_test_cmd += "diff -ru <(sort output/evidence.gff) <(sort test/evidence.gff)" + +sanity_check_commands = [ + "prothint.py --help", + local_test_cmd, +] + +moduleclass = 'bio' From 824d575fade3e55613aa32d3dc0e3ad4cdd4820c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 22:29:13 +0200 Subject: [PATCH 311/431] adding easyconfigs: popscle-0.1-beta-foss-2019b.eb and patches: popscle-0.1-beta_fix-compilation-GCC-8.3.patch --- .../p/popscle/popscle-0.1-beta-foss-2019b.eb | 47 +++++++++++++++++++ ...cle-0.1-beta_fix-compilation-GCC-8.3.patch | 39 +++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/p/popscle/popscle-0.1-beta-foss-2019b.eb create mode 100644 easybuild/easyconfigs/p/popscle/popscle-0.1-beta_fix-compilation-GCC-8.3.patch diff --git a/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-foss-2019b.eb b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-foss-2019b.eb new file mode 100644 index 00000000000..6673065bef5 --- /dev/null +++ b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-foss-2019b.eb @@ -0,0 +1,47 @@ +# Author: Arne Soete +# VIB-UGent Center for Inflammation Research + +easyblock = 'CMakeMake' + +name = 'popscle' +version = '0.1-beta' + +homepage = 'https://github.com/statgen/popscle' +description = """A suite of +population scale analysis tools for single-cell genomics data including +implementation of Demuxlet / Freemuxlet methods and auxilary tools """ + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True, 'cstd': 'c++14'} + +source_urls = ['https://github.com/statgen/popscle/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['popscle-%(version)s_fix-compilation-GCC-8.3.patch'] +checksums = [ + '67e1191efd879e860ba546487180857d904fe14a79b49f6541a557de4779ba00', # v0.1-beta.tar.gz + # popscle-0.1-beta_fix-compilation-GCC-8.3.patch + '2f03f445cc37aee3e33af087c3b1bb43f1bd09bb02e98e064bd27d89289cdcfe', +] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('HTSlib', '1.10.2'), + ('XZ', '5.2.4'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHTS_INCLUDE_DIRS=$EBROOTHTSLIB/include -DHTS_LIBRARIES=$EBROOTHTSLIB/lib/libhts.a " +configopts += "-DBZIP2_INCLUDE_DIRS=$EBROOTBZIP2/include -DBZIP2_LIBRARIES=$EBROOTBZIP2/lib/libbz2.a " +configopts += "-DLZMA_INCLUDE_DIRS=$EBROOTXZ/include -DLZMA_LIBRARIES=$EBROOTXZ/lib/liblzma.a " + +install_cmd = "mkdir %(installdir)s/bin && install %(builddir)s/%(name)s-%(version)s/bin/popscle %(installdir)s/bin/" + +sanity_check_paths = { + 'files': ['bin/popscle'], + 'dirs': [], +} + +sanity_check_commands = ["popscle --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/popscle/popscle-0.1-beta_fix-compilation-GCC-8.3.patch b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta_fix-compilation-GCC-8.3.patch new file mode 100644 index 00000000000..1a71a51ceeb --- /dev/null +++ b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta_fix-compilation-GCC-8.3.patch @@ -0,0 +1,39 @@ +fix compilation with GCC 8.3.0, see https://github.com/statgen/popscle/issues/27 + +author: Lars Viklund (Umeå University) +diff --git a/gtf.h b/gtf.h +index 1df030d..03d713d 100644 +--- a/gtf.h ++++ b/gtf.h +@@ -201,7 +201,8 @@ public: + }; + + struct gtfComp { +- bool operator()(const gtfElement* lhs, const gtfElement* rhs) const { ++ template // required as element may be of incomplete type at point of instantiation ++ bool operator()(const T* lhs, const T* rhs) const { + if ( lhs->locus == rhs->locus ) { + return ((int64_t)rhs - (int64_t)lhs > 0); + } +diff --git a/sam_ordered_writer.cpp b/sam_ordered_writer.cpp +index d2e380c..76e584e 100644 +--- a/sam_ordered_writer.cpp ++++ b/sam_ordered_writer.cpp +@@ -135,7 +135,7 @@ void SAMOrderedWriter::write(bam1_t *v) + + if (i==buffer.end()) + { +- int32_t cutoff_pos1 = std::max(bam_get_pos1(buffer.front())-window,1); ++ int32_t cutoff_pos1 = std::max(bam_get_pos1(buffer.front())-window,1); + if (bam_get_pos1(v)1) { +- int32_t cutoff_pos1 = std::max(bam_get_pos1(buffer.front())-window,1); ++ int32_t cutoff_pos1 = std::max(bam_get_pos1(buffer.front())-window,1); + + while (buffer.size()>1) { + if (bam_get_pos1(buffer.back())<=cutoff_pos1) { From 1a6503c24c238178a8b66c381f27af70ab7adf78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Apr 2020 22:47:24 +0200 Subject: [PATCH 312/431] adding easyconfigs: bcl2fastq2-2.20.0-GCC-8.3.0.eb --- .../bcl2fastq2/bcl2fastq2-2.20.0-GCC-8.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-8.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-8.3.0.eb new file mode 100644 index 00000000000..fc3a194b39c --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-8.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] + +checksums = ['8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3'] + +# CMake, Boost, libxml2 and libxslt are all built and used internally with specific versions +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'src' +configopts = '--force-builddir' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'] +} + +moduleclass = 'bio' From 600a3c215959e8a1c7cea5ff52d12ee86a49803e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 May 2020 08:21:33 +0200 Subject: [PATCH 313/431] adding easyconfigs: VTK-8.2.0-foss-2020a-Python-3.8.2.eb, VTK-8.2.0-intel-2020a-Python-3.8.2.eb --- .../VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb | 97 +++++++++++++++++++ .../VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb | 97 +++++++++++++++++++ 2 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..268ad67bac1 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,97 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz + 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('XZ', '5.2.5'), + ('HDF5', '1.10.6'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20200222'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1b0e8c36287 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,97 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = ['VTK-8.2.0_python_3.8_compatibility.patch', ('vtk-version.egg-info', '.')] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz + 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('XZ', '5.2.5'), + ('HDF5', '1.10.6'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20200222'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' From 6f1d162f158fc50012acde121cda634a9399d59a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 May 2020 08:22:26 +0200 Subject: [PATCH 314/431] adding easyconfigs: GDAL-3.0.4-foss-2020a-Python-3.8.2.eb, GDAL-3.0.4-intel-2020a-Python-3.8.2.eb, GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb --- .../GDAL-3.0.4-foss-2020a-Python-3.8.2.eb | 61 ++++++++++++++++++ .../GDAL-3.0.4-intel-2020a-Python-3.8.2.eb | 63 +++++++++++++++++++ ...-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb | 33 ++++++++++ 3 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..f60ac42d5a0 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277', # gdal-3.0.4.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.8.1', versionsuffix), + ('SQLite', '3.31.1'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.69.1'), + ('PCRE', '8.44'), + ('PROJ', '7.0.0'), + ('libgeotiff', '1.5.1'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..7cd0e55a80d --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '5569a4daa1abcbba47a9d535172fc335194d9214fdb96cd0f139bb57329ae277', # gdal-3.0.4.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('netCDF', '4.7.4'), + ('expat', '2.2.9'), + ('GEOS', '3.8.1', versionsuffix), + ('SQLite', '3.31.1'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.1.0'), + ('zlib', '1.2.11'), + ('cURL', '7.69.1'), + ('PCRE', '8.44'), + ('PROJ', '7.0.0'), + ('libgeotiff', '1.5.1'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +prebuildopts = 'export LDSHARED="$CC -shared" && ' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb new file mode 100644 index 00000000000..0bf4e9a4ce9 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.1-iccifort-2020.1.217-Python-3.8.2.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-3.7.2_fix-Python3.patch'] +checksums = [ + '4258af4308deb9dbb5047379026b4cd9838513627cb943a44e16c40e42ae17f7', # geos-3.8.1.tar.bz2 + 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch +] + +dependencies = [('Python', '3.8.2')] + +builddependencies = [('SWIG', '4.0.1')] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' From ae3a1c7b3c7a98829c8a98d4234ba9a982c50fc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 May 2020 08:25:54 +0200 Subject: [PATCH 315/431] {chem}[foss/2020a,intel/2020a] PLUMED v2.6.0 w/ Python 3.8.2 --- .../g/GSL/GSL-2.6-iccifort-2020.1.217.eb | 25 ++++++++ .../PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb | 60 +++++++++++++++++++ .../PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb | 60 +++++++++++++++++++ 3 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb new file mode 100644 index 00000000000..af6a5a7298c --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.6-iccifort-2020.1.217.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.6' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b782339fc7a38fe17689cb39966c4d821236c28018b6593ddb6fd59ee40786a8'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..07c6e727d9e --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,60 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['8a760a637225eeb97e84b748e992ebc0730f71cdb4737af545445132380bfff9'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Boost', '1.72.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..c7b659d56d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,60 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['8a760a637225eeb97e84b748e992ebc0730f71cdb4737af545445132380bfff9'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Boost', '1.72.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From ad8039f1b74573fec9ff8bb0a07b010a2ecf1d94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 May 2020 08:42:18 +0200 Subject: [PATCH 316/431] add missing patch file for VTK 8.2.0 --- .../VTK-8.2.0_python_3.8_compatibility.patch | 176 ++++++++++++++++++ 1 file changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch b/easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch new file mode 100644 index 00000000000..60134b1fee1 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0_python_3.8_compatibility.patch @@ -0,0 +1,176 @@ +From 257b9d7b18d5f3db3fe099dc18f230e23f7dfbab Mon Sep 17 00:00:00 2001 +From: David Gobbi +Date: Tue, 20 Aug 2019 17:02:24 -0600 +Subject: [PATCH] Compatibility for Python 3.8 + +The PyTypeObject struct was modified in Python 3.8, this change is +required to avoid compile errors. +--- + .../PythonInterpreter/vtkPythonStdStreamCaptureHelper.h | 6 ++++++ + Wrapping/PythonCore/PyVTKMethodDescriptor.cxx | 2 +- + Wrapping/PythonCore/PyVTKNamespace.cxx | 2 +- + Wrapping/PythonCore/PyVTKReference.cxx | 8 ++++---- + Wrapping/PythonCore/PyVTKTemplate.cxx | 2 +- + Wrapping/PythonCore/vtkPythonCompatibility.h | 8 +++++++- + Wrapping/Tools/vtkWrapPythonClass.c | 2 +- + Wrapping/Tools/vtkWrapPythonEnum.c | 2 +- + Wrapping/Tools/vtkWrapPythonType.c | 2 +- + 9 files changed, 23 insertions(+), 11 deletions(-) + +diff --git a/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h b/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h +index b1c12c83de..14ccfbe928 100644 +--- a/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h ++++ b/Utilities/PythonInterpreter/vtkPythonStdStreamCaptureHelper.h +@@ -140,6 +140,12 @@ static PyTypeObject vtkPythonStdStreamCaptureHelperType = { + #if PY_VERSION_HEX >= 0x03040000 + 0, // tp_finalize + #endif ++#if PY_VERSION_HEX >= 0x03080000 ++ 0, // tp_vectorcall ++#if PY_VERSION_HEX < 0x03090000 ++ 0, // tp_print ++#endif ++#endif + }; + + static PyObject* vtkWrite(PyObject* self, PyObject* args) +diff --git a/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx b/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx +index 2b0d443537..3840038498 100644 +--- a/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx ++++ b/Wrapping/PythonCore/PyVTKMethodDescriptor.cxx +@@ -186,7 +186,7 @@ PyTypeObject PyVTKMethodDescriptor_Type = { + sizeof(PyMethodDescrObject), // tp_basicsize + 0, // tp_itemsize + PyVTKMethodDescriptor_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/PyVTKNamespace.cxx b/Wrapping/PythonCore/PyVTKNamespace.cxx +index 71ee2a3516..5cf5bfbe6b 100644 +--- a/Wrapping/PythonCore/PyVTKNamespace.cxx ++++ b/Wrapping/PythonCore/PyVTKNamespace.cxx +@@ -49,7 +49,7 @@ PyTypeObject PyVTKNamespace_Type = { + 0, // tp_basicsize + 0, // tp_itemsize + PyVTKNamespace_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/PyVTKReference.cxx b/Wrapping/PythonCore/PyVTKReference.cxx +index 943ac71080..b7104091c0 100644 +--- a/Wrapping/PythonCore/PyVTKReference.cxx ++++ b/Wrapping/PythonCore/PyVTKReference.cxx +@@ -1010,7 +1010,7 @@ PyTypeObject PyVTKReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +@@ -1067,7 +1067,7 @@ PyTypeObject PyVTKNumberReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +@@ -1124,7 +1124,7 @@ PyTypeObject PyVTKStringReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +@@ -1181,7 +1181,7 @@ PyTypeObject PyVTKTupleReference_Type = { + sizeof(PyVTKReference), // tp_basicsize + 0, // tp_itemsize + PyVTKReference_Delete, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/PyVTKTemplate.cxx b/Wrapping/PythonCore/PyVTKTemplate.cxx +index be200985b3..340fe7953b 100644 +--- a/Wrapping/PythonCore/PyVTKTemplate.cxx ++++ b/Wrapping/PythonCore/PyVTKTemplate.cxx +@@ -268,7 +268,7 @@ PyTypeObject PyVTKTemplate_Type = { + 0, // tp_basicsize + 0, // tp_itemsize + nullptr, // tp_dealloc +- nullptr, // tp_print ++ 0, // tp_vectorcall_offset + nullptr, // tp_getattr + nullptr, // tp_setattr + nullptr, // tp_compare +diff --git a/Wrapping/PythonCore/vtkPythonCompatibility.h b/Wrapping/PythonCore/vtkPythonCompatibility.h +index 4a767844a6..be208faeef 100644 +--- a/Wrapping/PythonCore/vtkPythonCompatibility.h ++++ b/Wrapping/PythonCore/vtkPythonCompatibility.h +@@ -64,7 +64,13 @@ + #endif + + // PyTypeObject compatibility +-#if PY_VERSION_HEX >= 0x03040000 ++#if PY_VERSION_HEX >= 0x03090000 ++#define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \ ++ 0, 0, 0, 0, ++#elif PY_VERSION_HEX >= 0x03080000 ++#define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \ ++ 0, 0, 0, 0, 0, ++#elif PY_VERSION_HEX >= 0x03040000 + #define VTK_WRAP_PYTHON_SUPPRESS_UNINITIALIZED \ + 0, 0, 0, + #else +diff --git a/Wrapping/Tools/vtkWrapPythonClass.c b/Wrapping/Tools/vtkWrapPythonClass.c +index b1e45f8e80..4d558ea081 100644 +--- a/Wrapping/Tools/vtkWrapPythonClass.c ++++ b/Wrapping/Tools/vtkWrapPythonClass.c +@@ -521,7 +521,7 @@ void vtkWrapPython_GenerateObjectType( + " sizeof(PyVTKObject), // tp_basicsize\n" + " 0, // tp_itemsize\n" + " PyVTKObject_Delete, // tp_dealloc\n" +- " nullptr, // tp_print\n" ++ " 0, // tp_vectorcall_offset\n" + " nullptr, // tp_getattr\n" + " nullptr, // tp_setattr\n" + " nullptr, // tp_compare\n" +diff --git a/Wrapping/Tools/vtkWrapPythonEnum.c b/Wrapping/Tools/vtkWrapPythonEnum.c +index b933702242..1249362854 100644 +--- a/Wrapping/Tools/vtkWrapPythonEnum.c ++++ b/Wrapping/Tools/vtkWrapPythonEnum.c +@@ -145,7 +145,7 @@ void vtkWrapPython_GenerateEnumType( + " sizeof(PyIntObject), // tp_basicsize\n" + " 0, // tp_itemsize\n" + " nullptr, // tp_dealloc\n" +- " nullptr, // tp_print\n" ++ " 0, // tp_vectorcall_offset\n" + " nullptr, // tp_getattr\n" + " nullptr, // tp_setattr\n" + " nullptr, // tp_compare\n" +diff --git a/Wrapping/Tools/vtkWrapPythonType.c b/Wrapping/Tools/vtkWrapPythonType.c +index 744cb1b9d3..0a1375e541 100644 +--- a/Wrapping/Tools/vtkWrapPythonType.c ++++ b/Wrapping/Tools/vtkWrapPythonType.c +@@ -709,7 +709,7 @@ void vtkWrapPython_GenerateSpecialType( + " sizeof(PyVTKSpecialObject), // tp_basicsize\n" + " 0, // tp_itemsize\n" + " Py%s_Delete, // tp_dealloc\n" +- " nullptr, // tp_print\n" ++ " 0, // tp_vectorcall_offset\n" + " nullptr, // tp_getattr\n" + " nullptr, // tp_setattr\n" + " nullptr, // tp_compare\n" +-- +2.24.1 + From 7c9ca35dca91f33c1ec9f6c491125bb651c2ed0c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 1 May 2020 16:42:58 +0200 Subject: [PATCH 317/431] make sure wolframscript is in the PATH for Mathematica-12.0.0 --- .../easyconfigs/m/Mathematica/Mathematica-12.0.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb index 3e349754db8..65e0b2bfc4a 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb @@ -1,7 +1,7 @@ name = 'Mathematica' version = '12.0.0' -homepage = 'http://www.wolfram.com/mathematica' +homepage = 'https://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" @@ -12,6 +12,11 @@ checksums = ['b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7'] license_server = 'license.example.com' -sanity_check_commands = [('mathematica', '--version')] +postinstallcmds = ['ln -s %(installdir)s/Executables/wolframscript %(installdir)s/bin/'] + +sanity_check_commands = [ + 'mathematica --version', + 'wolframscript -code "x=1"', +] moduleclass = 'math' From bc38dfe715a3b6911e2187227a13c7b149caef47 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 1 May 2020 17:38:23 +0200 Subject: [PATCH 318/431] remove extra sanity check command --- easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb index 65e0b2bfc4a..73b83549ef7 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb @@ -14,9 +14,6 @@ license_server = 'license.example.com' postinstallcmds = ['ln -s %(installdir)s/Executables/wolframscript %(installdir)s/bin/'] -sanity_check_commands = [ - 'mathematica --version', - 'wolframscript -code "x=1"', -] +sanity_check_commands = ['mathematica --version'] moduleclass = 'math' From 463adb789988ab3044585419de7d2941e1a8b009 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 May 2020 19:32:16 +0200 Subject: [PATCH 319/431] adding easyconfigs: molmod-1.4.5-foss-2020a-Python-3.8.2.eb, molmod-1.4.5-intel-2020a-Python-3.8.2.eb, yaff-1.6.0-foss-2020a-Python-3.8.2.eb, yaff-1.6.0-intel-2020a-Python-3.8.2.eb, h5py-2.10.0-foss-2020a-Python-3.8.2.eb, h5py-2.10.0-intel-2020a-Python-3.8.2.eb --- .../h5py-2.10.0-foss-2020a-Python-3.8.2.eb | 37 +++++++++++++++ .../h5py-2.10.0-intel-2020a-Python-3.8.2.eb | 37 +++++++++++++++ .../molmod-1.4.5-foss-2020a-Python-3.8.2.eb | 37 +++++++++++++++ .../molmod-1.4.5-intel-2020a-Python-3.8.2.eb | 40 ++++++++++++++++ .../yaff-1.6.0-foss-2020a-Python-3.8.2.eb | 47 +++++++++++++++++++ .../yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 47 +++++++++++++++++++ 6 files changed, 245 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..010d200891a --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] + +builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +use_pip = False +download_dep_fail = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) +options = {'modulename': False} +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..71353b9b531 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] + +builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +use_pip = False +download_dep_fail = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) +options = {'modulename': False} +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..8e0da02f6d7 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.5_deprecated_time_method.patch'] +checksums = [ + '69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c', # molmod-1.4.5.tar.gz + '7de0dae2accd908ff7b40f5f848ffabdb9267dadbfb8cc4d2d98444995282e2d', # molmod-1.4.5_deprecated_time_method.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..369862bf7c7 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.5_deprecated_time_method.patch'] +checksums = [ + '69c625fe081ea498371642d6237a8958cfc89608908fa8daa475f5d9dc5dc47c', # molmod-1.4.5.tar.gz + '7de0dae2accd908ff7b40f5f848ffabdb9267dadbfb8cc4d2d98444995282e2d', # molmod-1.4.5_deprecated_time_method.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..cf0cfcf3206 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,47 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this at non-interactive job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.2'), + ('h5py', '2.10.0', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..4846a904a7c --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,47 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this at non-interactive job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.2'), + ('h5py', '2.10.0', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From 855be4c3e0b88f735cd47ff9bff97f2e023d92d7 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sat, 2 May 2020 19:46:21 +0200 Subject: [PATCH 320/431] Tracking the name of the constants from the framework. --- .../p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb | 2 +- .../p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb index 93fb43172fe..49804b5a15b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ local_mkdir_and_extract_cmd_pattern = "DIR=%s/%s; mkdir -p $DIR; tar -C $DIR --s source_urls = ['https://github.com/pytorch/pytorch/archive'] -osdependencies = [OSPACKAGES_IBVERBS] +osdependencies = [OS_PKG_IBVERBS_DEV] # PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. # determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.4.0/third_party diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb index c496e380a34..5ad1d5713c6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ local_mkdir_and_extract_cmd_pattern = "DIR=%s/%s; mkdir -p $DIR; tar -C $DIR --s source_urls = ['https://github.com/pytorch/pytorch/archive'] -osdependencies = [OSPACKAGES_IBVERBS] +osdependencies = [OS_PKG_IBVERBS_DEV] # PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. # determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.4.0/third_party From b661d7bd85dabca16caabd27e73f05f4d58b4301 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 May 2020 20:36:18 +0200 Subject: [PATCH 321/431] disable tests in yaff easyconfig using intel/2020a toolchain + run import test via mpirun --- .../y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb index 4846a904a7c..f20b3e07aaf 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb @@ -36,12 +36,21 @@ sanity_pip_check = True # required because we're building a Python package using Intel compilers on top of Python built with GCC check_ldshared = True -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" +# disable tests when installing with intel/2020a, due to bug in Intel MPI 2019 update 7; +# commands that trigger an MPI_Init crash with "Fatal error in PMPI_Init_thread" if they're not run via mpirun, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/10213 +# runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +# runtest += "python setup.py build_ext -i; %(mpi_cmd_prefix)s nosetests -v" sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +# skip regular 'import yaff', and run it via mpirun (since 'import yaff' results in an MPI_Init call via h5py) +# this is only needed because of a bug in Intel MPI 2019 update 7 ("Fatal error in PMPI_Init_thread") +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/10213 +options = {'modulename': False} +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] + moduleclass = 'chem' From 58860c273a75dd5c30c60904340a48c403307647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 May 2020 20:38:09 +0200 Subject: [PATCH 322/431] add missing patch file for molmod --- .../molmod-1.4.5_deprecated_time_method.patch | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch new file mode 100644 index 00000000000..33594754c11 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.5_deprecated_time_method.patch @@ -0,0 +1,42 @@ +Molmod is not compatible with Python 3.8 due to its deprecated +use of time.clock() (which is no longer supported as of 3.8) + +Alan O'Cais, 20200324 +diff -Nru molmod-1.4.5.orig/molmod/log.py molmod-1.4.5/molmod/log.py +--- molmod-1.4.5.orig/molmod/log.py 2019-09-11 20:34:14.000000000 +0200 ++++ molmod-1.4.5/molmod/log.py 2020-03-20 10:05:41.874916780 +0100 +@@ -388,11 +388,11 @@ + + def start(self): + assert self._start is None +- self._start = time.clock() ++ self._start = time.process_time() + + def stop(self): + assert self._start is not None +- self.cpu += time.clock() - self._start ++ self.cpu += time.process_time() - self._start + self._start = None + + +diff -Nru molmod-1.4.5.orig/molmod/minimizer.py molmod-1.4.5/molmod/minimizer.py +--- molmod-1.4.5.orig/molmod/minimizer.py 2019-09-11 20:34:14.000000000 +0200 ++++ molmod-1.4.5/molmod/minimizer.py 2020-03-20 10:06:39.712207523 +0100 +@@ -1414,7 +1414,7 @@ + except ConstraintError: + self._screen("CONSTRAINT PROJECT FAILED", newline=True) + return False +- self.last_end = time.clock() ++ self.last_end = time.process_time() + + def propagate(self): + # compute the new direction +@@ -1474,7 +1474,7 @@ + else: + converged = False + # timing +- end = time.clock() ++ end = time.process_time() + self._screen("%5.2f" % (end - self.last_end), newline=True) + self.last_end = end + # check convergence, part 2 From abb109cd9df000797d8f4980868e8af1542133da Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 2 May 2020 21:20:01 +0000 Subject: [PATCH 323/431] adding easyconfigs: PyTables-3.6.1-fosscuda-2019b-Python-3.7.4.eb, numexpr-2.7.1-fosscuda-2019b-Python-3.7.4.eb --- ...mexpr-2.7.1-fosscuda-2019b-Python-3.7.4.eb | 22 +++++++++ ...ables-3.6.1-fosscuda-2019b-Python-3.7.4.eb | 46 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..fa5d0c7ccdd --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.7.1-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,22 @@ +name = 'numexpr' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c6ae3bb5688184b922b43fc47de49d642576d0feec55a1b679caa66efae90a1'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..6754ad448c5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('numexpr', '2.7.1', versionsuffix), + ('HDF5', '1.10.5'), + ('LZO', '2.10'), + ('Blosc', '1.17.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' From 9b559a47a38d388b4e05ae1dbfc87bc3abdadd16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 May 2020 10:17:20 +0200 Subject: [PATCH 324/431] clarify comments in yaff easyconfigs w.r.t. hang in Slurm interactive session --- .../easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb | 4 ++-- .../easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb index cf0cfcf3206..a1215832a8a 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb @@ -2,10 +2,10 @@ # Author: Pavel Grochal (INUITS) # License: GPLv2 # -# Building this in interactive session will result in freeze during either +# Building this in interactive Slurm session will result in freeze during either # runtest phase or sanity_check_commands phase (python -c 'import yaff') # -# If you submit this at non-interactive job, it will build just fine. +# If you submit this as non-interactive Slurm job, it will build just fine. # Possibly root cause: https://github.com/h5py/h5py/issues/917 # easyblock = 'PythonPackage' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb index f20b3e07aaf..162894aaf51 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb @@ -2,10 +2,10 @@ # Author: Pavel Grochal (INUITS) # License: GPLv2 # -# Building this in interactive session will result in freeze during either +# Building this in interactive Slurm session will result in freeze during either # runtest phase or sanity_check_commands phase (python -c 'import yaff') # -# If you submit this at non-interactive job, it will build just fine. +# If you submit this as non-interactive Slurm job, it will build just fine. # Possibly root cause: https://github.com/h5py/h5py/issues/917 # easyblock = 'PythonPackage' From ab2509ba08ba45cb91563ae67668f1e0eaf6d66d Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 3 May 2020 18:01:56 +0000 Subject: [PATCH 325/431] adding easyconfigs: openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb --- ...enpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..c54652ba74f --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), + ('lxml', '4.4.2'), + ('Pillow', '6.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('et_xmlfile', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/e/et_xmlfile'], + 'checksums': ['614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b'], + }), + ('jdcal', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/e/j/jdcal'], + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/o/openpyxl'], + 'checksums': ['547a9fc6aafcf44abe358b89ed4438d077e9d92e4f182c87e2dc294186dc4b64'], + }), +] + +moduleclass = 'data' From f7f471a414fd073176f12c6ead4324ec43814a89 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 3 May 2020 18:39:55 +0000 Subject: [PATCH 326/431] Remove download_dep_fail and sanity_pip_check --- .../o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb index c54652ba74f..d269e867f77 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -18,8 +18,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True -sanity_pip_check = True exts_list = [ ('et_xmlfile', '1.0.1', { From 4e9a8229208f91a472136ace9a30b74163c47ca0 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 3 May 2020 19:26:29 +0000 Subject: [PATCH 327/431] Add sanity_pip_check --- .../o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb index d269e867f77..60da7c2c8d1 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -18,6 +18,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('et_xmlfile', '1.0.1', { From e8882f0f11fde8f0b34a740213298e907c0f95c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 May 2020 08:56:35 +0200 Subject: [PATCH 328/431] add missing PyVCF dependency for BAMSurgeon --- .../BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb | 6 ++++ .../p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb index 20ce4bdd8d2..2aadd350563 100644 --- a/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb +++ b/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb @@ -21,6 +21,7 @@ dependencies = [ ('Velvet', '1.2.10', '-mt-kmer_191'), ('Exonerate', '2.4.0'), ('Pysam', '0.15.3'), + ('PyVCF', '0.6.8'), ] download_dep_fail = True @@ -33,6 +34,11 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + "evaluator.py --help", # requires PyVCF + "postprocess.py --help", +] + sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb new file mode 100644 index 00000000000..c7761dfa305 --- /dev/null +++ b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'PyVCF' +version = '0.6.8' + +homepage = 'https://github.com/jamescasbon/PyVCF' +description = "A Variant Call Format reader for Python." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +dependencies = [('Pysam', '0.15.3')] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'vcf'} + +sanity_check_paths = { + 'files': ['bin/vcf_filter.py', 'bin/vcf_melt', 'bin/vcf_sample_filter.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "vcf_filter.py --help", + "vcf_sample_filter.py --help" +] + +sanity_pip_check = True + +moduleclass = 'bio' From 1dba8070f8256f5ca27b18a10aa68ab49a665647 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 4 May 2020 09:14:55 +0200 Subject: [PATCH 329/431] easyblock can now detect FFTW or MKL (which are part of toolchain) --- .../l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb | 1 - .../l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 1 - .../l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb | 1 - .../l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index c4bf0a8a8dc..f4fd6fb61ec 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -53,7 +53,6 @@ dependencies = [ ('libxml2', '2.9.9'), ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), - ('FFTW', '3.3.8'), ('kim-api', '2.1.3'), ('Eigen', '3.3.7', '', True), ('yaff', '1.6.0', local_python_versionsuffix), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 68b41e024b5..d7f50c89fc7 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -53,7 +53,6 @@ dependencies = [ ('libxml2', '2.9.9'), ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), - ('FFTW', '3.3.8'), ('kim-api', '2.1.3'), ('Eigen', '3.3.7', '', True), ('yaff', '1.6.0', local_python_versionsuffix), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index d4671f247a2..434cd51f79d 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -53,7 +53,6 @@ dependencies = [ ('libxml2', '2.9.9'), ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), - ('FFTW', '3.3.8'), ('kim-api', '2.1.3'), ('Eigen', '3.3.7', '', True), ('yaff', '1.6.0', local_python_versionsuffix), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index aef05a7fcad..2f13aa1cd60 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -53,7 +53,6 @@ dependencies = [ ('libxml2', '2.9.9'), ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), - ('FFTW', '3.3.8'), ('kim-api', '2.1.3'), ('Eigen', '3.3.7', '', True), ('yaff', '1.6.0', local_python_versionsuffix), From 67bbd71c0fdaa24acb09268f873a9253a8ef6ed8 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Mon, 4 May 2020 09:38:02 +0200 Subject: [PATCH 330/431] adding easyconfigs: YAXT-0.6.2-foss-2018b.eb --- .../y/YAXT/YAXT-0.6.2-foss-2018b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-foss-2018b.eb diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-foss-2018b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-foss-2018b.eb new file mode 100644 index 00000000000..3794f2c8378 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-foss-2018b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.6.2' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/492/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7fc9b3e5dd2e0d3d5846f389a01c935aa40528eb09d82162b76c061b496a3c5b'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From 64d000292b9e0571aecc52ad8512ada90d8a5672 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Mon, 4 May 2020 09:40:27 +0200 Subject: [PATCH 331/431] adding easyconfigs: ecCodes-2.17.0-foss-2018b-Python-3.6.6.eb --- .../ecCodes-2.17.0-foss-2018b-Python-3.6.6.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..cea942ba135 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.17.0' +versionsuffix = '-Python-3.6.6' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['762d6b71993b54f65369d508f88e4c99e27d2c639c57a5978c284c49133cc335'] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [ + ('netCDF', '4.6.1'), + ('JasPer', '2.0.14'), + ('Python', '3.6.6'), +] + +separate_build_dir = True + +configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON -DENABLE_PYTHON=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +moduleclass = 'tools' From f13427705b1e25e741ce85b095816a2973e46303 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Mon, 4 May 2020 10:41:20 +0200 Subject: [PATCH 332/431] adding easyconfigs: YAXT-0.6.2-gompi-2019b.eb --- .../y/YAXT/YAXT-0.6.2-gompi-2019b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-gompi-2019b.eb diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-gompi-2019b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-gompi-2019b.eb new file mode 100644 index 00000000000..25c83bc0a28 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.2-gompi-2019b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.6.2' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/492/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7fc9b3e5dd2e0d3d5846f389a01c935aa40528eb09d82162b76c061b496a3c5b'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From e089f343574b7fe249644f27cc434d463f27a96c Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Mon, 4 May 2020 10:43:15 +0200 Subject: [PATCH 333/431] adding easyconfigs: ecCodes-2.17.0-foss-2019b-Python-3.7.4.eb --- .../ecCodes-2.17.0-foss-2019b-Python-3.7.4.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..14fcb1c91f0 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.17.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.17.0' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['762d6b71993b54f65369d508f88e4c99e27d2c639c57a5978c284c49133cc335'] + +builddependencies = [('CMake', '3.15.3')] +dependencies = [ + ('netCDF', '4.7.1'), + ('JasPer', '2.0.14'), + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', '-Python-3.7.4') +] + +separate_build_dir = True + +configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON -DENABLE_PYTHON=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +moduleclass = 'tools' From 82d7c483932e7898b545b1cefc404b42427c95c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 May 2020 11:45:13 +0200 Subject: [PATCH 334/431] adding easyconfigs: FastViromeExplorer-20180422-foss-2019b.eb --- .../FastViromeExplorer-20180422-foss-2019b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb diff --git a/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb b/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb new file mode 100644 index 00000000000..0fad82d9d44 --- /dev/null +++ b/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb @@ -0,0 +1,38 @@ +easyblock = 'CmdCp' + +name = 'FastViromeExplorer' +local_commit = 'aeb2a868' +version = '20180422' + +homepage = 'https://code.vt.edu/saima5/FastViromeExplorer' +description = "Identify the viruses/phages and their abundance in the viral metagenomics data." + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://code.vt.edu/saima5/FastViromeExplorer/-/archive/%s' % local_commit] +sources = [{'download_filename': 'FastViromeExplorer-%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['3a8e7842e83539cd36f619f1e01761e2c5b87a44a5f51328287b6dd20ef47384'] + +dependencies = [ + ('Java', '11', '', True), + ('kallisto', '0.46.1'), + ('SAMtools', '1.10'), +] + +cmds_map = [('.*', "javac -d bin src/*.java")] +files_to_copy = ['bin', '*.txt', 'test', 'utility-scripts', 'README.md'] + +sanity_check_paths = { + 'files': ['bin/FastViromeExplorer.class', 'ncbi-viruses-list.txt'], + 'dirs': ['test', 'utility-scripts'], +} + +# see https://code.vt.edu/saima5/FastViromeExplorer/tree/master#run-fastviromeexplorer-using-test-data +local_test_cmd = "cd %(builddir)s && cp -a FastViromeExplorer-*/{test,ncbi-viruses-list.txt} . && " +local_test_cmd += "java FastViromeExplorer -1 test/reads_1.fq -2 test/reads_2.fq " +local_test_cmd += "-i test/testset-kallisto-index.idx -o test-output" +sanity_check_commands = [local_test_cmd] + +modextrapaths = {'CLASSPATH': ['bin']} + +moduleclass = 'bio' From e2e696fc982ba693c1139dd494d8bb85651c9ca6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 May 2020 17:54:59 +0200 Subject: [PATCH 335/431] adding easyconfigs: Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb --- ...-5.0.1-20200316-foss-2019b-Python-3.7.4.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..cf5aaa87f68 --- /dev/null +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'Taiyaki' +local_commit = '486b76a' +version = '5.0.1-20200316' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/taiyaki' +description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('Pysam', '0.15.3'), + ('PyTorch', '1.4.0', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('statsmodels', '0.11.1', { + 'checksums': ['5bde3fa0a35a91b45dba7cbc28270b5b649ff1d721c89290883f6e831672d5f0'], + }), + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + ('ont-fast5-api', '3.1.1', { + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), + (name, version, { + 'source_tmpl': '486b76a.tar.gz', + 'source_urls': ['https://github.com/nanoporetech/taiyaki/archive/'], + 'checksums': ['5fe92fd7db2311ef3c59b1e77275a434ad3ee8107c918f5937746a6ca7615e00'], + 'preinstallopts': "sed -i 's/torch == 1.2/torch/g' setup.py && " + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/basecall.py', 'bin/prepare_mapped_reads.py', 'bin/train_flipflop.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 2d42b7fe8bae47fb795f861d37930c8798396c26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 May 2020 17:55:27 +0200 Subject: [PATCH 336/431] adding easyconfigs: Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb, Biopython-1.75-fosscuda-2019b-Python-3.7.4.eb --- ...python-1.75-fosscuda-2019b-Python-3.7.4.eb | 54 +++++++++++++++++ ....1-20200316-fosscuda-2019b-Python-3.7.4.eb | 58 +++++++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.75-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.75-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.75-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0a389e4de60 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.75-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,54 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , +# Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +# Updated: Pavel Grochal (INUITS) +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.75' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5060e4ef29c2bc214749733634051be5b8d11686c6590fa155c3443dcaa89906'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # for numpy +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..74f4915ce39 --- /dev/null +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'Taiyaki' +local_commit = '486b76a' +version = '5.0.1-20200316' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/taiyaki' +description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('Pysam', '0.15.3'), + ('PyTorch', '1.4.0', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('statsmodels', '0.11.1', { + 'checksums': ['5bde3fa0a35a91b45dba7cbc28270b5b649ff1d721c89290883f6e831672d5f0'], + }), + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + ('ont-fast5-api', '3.1.1', { + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), + (name, version, { + 'source_tmpl': '486b76a.tar.gz', + 'source_urls': ['https://github.com/nanoporetech/taiyaki/archive/'], + 'checksums': ['5fe92fd7db2311ef3c59b1e77275a434ad3ee8107c918f5937746a6ca7615e00'], + 'preinstallopts': "sed -i 's/torch == 1.2/torch/g' setup.py && " + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/basecall.py', 'bin/prepare_mapped_reads.py', 'bin/train_flipflop.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 4c3b30d3252f0e5653a2475bd309fab3005181a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 May 2020 18:32:38 +0200 Subject: [PATCH 337/431] stick to PyTorch 1.3.1 in Taiyaki easyconfig usign foss/2019b toolchain --- .../t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb index cf5aaa87f68..0edb2e0be25 100644 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ dependencies = [ ('h5py', '2.10.0', versionsuffix), ('Biopython', '1.75', versionsuffix), ('Pysam', '0.15.3'), - ('PyTorch', '1.4.0', versionsuffix), + ('PyTorch', '1.3.1', versionsuffix), ('matplotlib', '3.1.1', versionsuffix), ] From 9b34a4c663b04f10412d7e0bf35951e607042b10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 May 2020 18:34:18 +0200 Subject: [PATCH 338/431] stick to PyTorch 1.3.1 in Taiyaki easyconfig usign fosscuda/2019b toolchain --- .../Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb index 74f4915ce39..989abf0702b 100644 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ dependencies = [ ('h5py', '2.10.0', versionsuffix), ('Biopython', '1.75', versionsuffix), ('Pysam', '0.15.3'), - ('PyTorch', '1.4.0', versionsuffix), + ('PyTorch', '1.3.1', versionsuffix), ('matplotlib', '3.1.1', versionsuffix), ] From 210153e59c0cba16e2b886fb9ad8b8691a868b28 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 4 May 2020 19:02:51 +0200 Subject: [PATCH 339/431] adding easyconfigs: NCIPLOT-4.0-20200106-iccifort-2019.5.281.eb --- ...CIPLOT-4.0-20200106-iccifort-2019.5.281.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200106-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200106-iccifort-2019.5.281.eb b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200106-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..a5f08bb3e84 --- /dev/null +++ b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200106-iccifort-2019.5.281.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'NCIPLOT' +local_ver = '4.0' +version = '%s-20200106' % local_ver +local_commit = '583aebe' + +homepage = 'https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html' +description = """ NCIPLOT is a program for revealing non covalent interactions + based on the reduced density gradient. """ + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/juliacontrerasgarcia/nciplot/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['c839bb145d716dcb1d2e021f9c58eea1a72d1b538d8114aa33b886ea6308bcac'] + +start_dir = 'src_%%(namelower)s_%s' % local_ver + +prebuildopts = "sed -i 's/include Makefile.inc//g' Makefile && " +prebuildopts += "sed -i 's/nciplot: $(OBJS) $(LIBS)/nciplot: $(OBJS)/g' Makefile && " +buildopts = 'LIBS="$LIBS" LDFLAGS="$LDFLAGS"' + +files_to_copy = ['dat', 'LICENSE', (['nciplot'], 'bin')] + +modextrapaths = {'NCIPLOT_HOME': ''} + +sanity_check_paths = { + 'files': ['bin/nciplot'], + 'dirs': ['dat'], +} + +modloadmsg = """ +Set environment variable OMP_NUM_THREADS equal to the number of available cores before running this program. +""" + +moduleclass = 'chem' From 295ca8aa89728e46be1e0ee26b6accb355d865dd Mon Sep 17 00:00:00 2001 From: software Date: Mon, 4 May 2020 20:54:03 +0000 Subject: [PATCH 340/431] adding easyconfigs: Rust-1.42.0-GCCcore-8.2.0.eb --- .../r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..18a3fc7c04f --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.42.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +moduleclass = 'lang' From d2b6da6fc0ff7c3741faaf78410784262154d9c1 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 4 May 2020 21:00:08 +0000 Subject: [PATCH 341/431] adding easyconfigs: libcroco-0.6.13-foss-2019a.eb, librsvg-2.48.4-foss-2019a.eb --- .../l/libcroco/libcroco-0.6.13-foss-2019a.eb | 27 ++++++++++++++++ .../l/librsvg/librsvg-2.48.4-foss-2019a.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-foss-2019a.eb create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.48.4-foss-2019a.eb diff --git a/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-foss-2019a.eb b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-foss-2019a.eb new file mode 100644 index 00000000000..b78c94750a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libcroco/libcroco-0.6.13-foss-2019a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libcroco' +version = '0.6.13' + +homepage = 'https://github.com/GNOME/libcroco' +description = """Libcroco is a standalone css2 parsing and manipulation library.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/libcroco/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['767ec234ae7aa684695b3a735548224888132e063f92db585759b422570621d4'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.8'), + ('GLib', '2.60.1'), +] + +sanity_check_paths = { + 'files': ['bin/csslint-%(version_major_minor)s', 'lib/libcroco-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libcroco-%(version_major_minor)s.a'], + 'dirs': ['include/libcroco-%(version_major_minor)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.48.4-foss-2019a.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.48.4-foss-2019a.eb new file mode 100644 index 00000000000..5c714a01b40 --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.48.4-foss-2019a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.48.4' + +homepage = 'https://wiki.gnome.org/action/show/Projects/LibRsvg' +description = """librsvg is a library to render SVG files using cairo.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['28b63af85ced557383d3d3ece6e1f6938720dee1ecfa40d926bf1de4747c956e'] + +dependencies = [ + ('Gdk-Pixbuf', '2.38.1'), + ('libcroco', '0.6.13'), + ('Pango', '1.43.0'), + ('cairo', '1.16.0'), + ('Rust', '1.42.0'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] + +# this loader wants to install in the directory of Gdk-Pixbuf itself, so disable +configopts = '--disable-pixbuf-loader' + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, 'lib/librsvg-2.a'], + 'dirs': ['include/librsvg-2.0', 'share'] +} + +moduleclass = 'vis' From a1a0f7a8b5151e89824b4a348a672dbdea466167 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 5 May 2020 01:17:17 +0200 Subject: [PATCH 342/431] Whitespace at EOF to retrigger tests after https://github.com/easybuilders/easybuild-framework/pull/3309 was merged. --- .../p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb | 1 + .../p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb index 49804b5a15b..a7c23f97ab8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb @@ -302,3 +302,4 @@ sanity_check_paths = { sanity_pip_check = True moduleclass = 'devel' + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb index 5ad1d5713c6..825b4aa9b06 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb @@ -308,3 +308,4 @@ sanity_check_paths = { sanity_pip_check = True moduleclass = 'devel' + From 535f76c31d1cba2927fcdd5bcb75dfa29a817bec Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 5 May 2020 01:33:09 +0200 Subject: [PATCH 343/431] And remove EOF whitespace. --- .../p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb | 1 - .../p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb index a7c23f97ab8..49804b5a15b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb @@ -302,4 +302,3 @@ sanity_check_paths = { sanity_pip_check = True moduleclass = 'devel' - diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb index 825b4aa9b06..5ad1d5713c6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb @@ -308,4 +308,3 @@ sanity_check_paths = { sanity_pip_check = True moduleclass = 'devel' - From 15abade5293f778f563e52d3bd7d9186d00b42f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 5 May 2020 08:53:53 +0200 Subject: [PATCH 344/431] adding easyconfigs: Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb --- ...aken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..da6339de567 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.0.9-beta' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.ccb.jhu.edu/software/%(namelower)s/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch'] +checksums = [ + '0287cf4df4b5d5511a9132d9ab37a8d76864bae445579efb9cb76db7e9c09eba', # v2.0.9-beta.tar.gz + '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2', # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch +] + +dependencies = [ + ('Perl', '5.28.0'), + ('BLAST+', '2.7.1'), + ('wget', '1.20.1'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s' + +sanity_check_paths = { + 'files': [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 29295c7d64961b143fe643a5962254ee2afd1355 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 5 May 2020 13:41:10 +0000 Subject: [PATCH 345/431] Meme updated to version 5.1.1 --- ...1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb | 39 +++++++++++++++++++ ....1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb new file mode 100644 index 00000000000..07ae04b54ba --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb @@ -0,0 +1,39 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.1.1' +versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['38d73d256d431ad4eb7da2c817ce56ff2b4e26c39387ff0d6ada088938b38eb5'] + +dependencies = [ + ('libxml2', '2.9.9'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Perl', '5.30.0'), + ('Python', '3.7.4') +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' + +sanity_check_paths = { + 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb new file mode 100644 index 00000000000..8eefbb8b55f --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb @@ -0,0 +1,39 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.1.1' +versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['38d73d256d431ad4eb7da2c817ce56ff2b4e26c39387ff0d6ada088938b38eb5'] + +dependencies = [ + ('libxml2', '2.9.9'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Perl', '5.30.0'), + ('Python', '3.7.4') +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' + +sanity_check_paths = { + 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' From 180c549911d2ffe7cf252889e5caba87651b9b3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 17:57:48 +0200 Subject: [PATCH 346/431] adding easyconfigs: Nextflow-20.04.1.eb --- .../n/Nextflow/Nextflow-20.04.1.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb new file mode 100644 index 00000000000..cf8212fe26f --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# Software License:: Apache v2.0 +# +# Notes:: Adapted from Author: @J. Sassmannshausen (Crick HPC team), +# updated to 20.01.0 by Kenneth Hoste (HPC-UGent) +## + +easyblock = 'CmdCp' + +name = 'Nextflow' +version = '20.04.1' + +homepage = 'https://www.nextflow.io' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ec939568585454cad3ab1a4f6510f0dee707e02ce44324bd43a05e5601d28136'] + +# specify dependency on Java/11 "wrapper", rather than a specific Java version +dependencies = [('Java', '11', '', True)] + +skipsteps = ['configure', 'build'] + +_exe_files = ['nextflow', 'gradlew'] + +files_to_copy = [ + (_exe_files, '%(installdir)s/bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 8294a43478efc933f462503eec272d35d3b2e34f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 19:01:47 +0200 Subject: [PATCH 347/431] adding easyconfigs: LMfit-1.0.0-intel-2019b-Python-3.7.4.eb --- .../LMfit-1.0.0-intel-2019b-Python-3.7.4.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..15624a318d8 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.0-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = "Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python" + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('asteval', '0.9.18', { + 'checksums': ['5d64e18b8a72c2c7ae8f9b70d1f80b68bbcaa98c1c0d7047c35489d03209bc86'], + }), + ('uncertainties', '3.1.2', { + 'checksums': ['ba07c17a8a78cb58a47cd373079c7ea459f8b26cd474e29163b6ba0d72856a1e'], + }), + ('lmfit', version, { + 'checksums': ['aa005a3ed8fe759e89cba59c5e130b5ff0b73e9379c6d6b10240daabff706ed5'], + }), +] + +moduleclass = 'math' From 8b69c1f492c740867b66455511909e0ffc6005b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 20:33:45 +0200 Subject: [PATCH 348/431] add additional extensions to R 3.6.2 + R-bundle-Bioconductor 3.10 easyconfigs --- .../R-bundle-Bioconductor-3.10-foss-2019b.eb | 18 +++++++++ .../easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 39 +++++++++++++++++++ .../easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 39 +++++++++++++++++++ 3 files changed, 96 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb index 7ea95d1ae90..739f4d436c3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb @@ -669,6 +669,24 @@ exts_list = [ ('MEDIPS', '1.38.0', { 'checksums': ['be59fca359a681b3a5c2a89cef5948429deddfb4a3239895bf0d60c1f9545a94'], }), + ('cytolib', '1.8.0', { + 'checksums': ['6996000f2501817b247e0d3dab44e6ba3bf200cc83be9384e154a033138865fe'], + }), + ('flowCore', '1.52.1', { + 'checksums': ['e25ea2951b88878d453760cfa510d72bbd7299040685be628f94c78302eb7b22'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('metap', '1.3', { + 'checksums': ['7fcf148bfd77f445b2ee68cbd2367caaf991028d9843020c755dd11965adb5ca'], + }), + ('uwot', '0.1.8', { + 'checksums': ['ede6e061b43f9e1337c0132a5334082f4565ec1623bbb0eee1f738034346f0cb'], + }), + ('Seurat', '3.1.5', { + 'checksums': ['757ef0e7697734aac5769705bef80dc7b95f006cdf52ae7034309a05f11578d1'], + }), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index e5ea8d08605..d3fbe5cd8d1 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -2339,6 +2339,45 @@ exts_list = [ ('dHSIC', '2.1', { 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.0', { + 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.5.0', { + 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.3.0', { + 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.0.0', { + 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], + }), + ('leiden', '0.3.3', { + 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], + }), + ('future.apply', '1.4.0', { + 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], + }), + ('sctransform', '0.2.1', { + 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index fddca0ca57e..d50e89d6e73 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -2340,6 +2340,45 @@ exts_list = [ ('dHSIC', '2.1', { 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.0', { + 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.5.0', { + 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.3.0', { + 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.0.0', { + 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], + }), + ('leiden', '0.3.3', { + 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], + }), + ('future.apply', '1.4.0', { + 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], + }), + ('sctransform', '0.2.1', { + 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), # Specific packages for GPUs ('OpenCL', '0.1-3.1', { 'checksums': ['daff23d777a27cd9d2e67ca8f5db1d29940cf0422708c1ea7e2d9661e3d6ae6f'], From 168a1cb6197c48ef1e66f8136ebf46a1b395dacf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 20:35:13 +0200 Subject: [PATCH 349/431] add additional extensions to R 3.6.3 & R 4.0.0 extensions --- .../easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 39 +++++++++++++++++++ .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index 68ab1f11bc9..bbb2c2b8dbf 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -2333,6 +2333,45 @@ exts_list = [ ('dHSIC', '2.1', { 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.0', { + 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.5.0', { + 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.3.0', { + 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.0.0', { + 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], + }), + ('leiden', '0.3.3', { + 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], + }), + ('future.apply', '1.4.0', { + 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], + }), + ('sctransform', '0.2.1', { + 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index c38960af58c..6cb1cae0a1c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2346,6 +2346,45 @@ exts_list = [ ('dHSIC', '2.1', { 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.0', { + 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.5.0', { + 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.3.0', { + 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.0.0', { + 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], + }), + ('leiden', '0.3.3', { + 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], + }), + ('future.apply', '1.4.0', { + 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], + }), + ('sctransform', '0.2.1', { + 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), ] moduleclass = 'lang' From 9484e5dca1243ed9ca1723214290357137e84e0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 20:49:42 +0200 Subject: [PATCH 350/431] adding easyconfigs: GlimmerHMM-3.0.4c-GCC-8.3.0.eb --- .../GlimmerHMM/GlimmerHMM-3.0.4c-GCC-8.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-8.3.0.eb new file mode 100644 index 00000000000..4269158b9ea --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-8.3.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' From 1d599a0213687082045493bc296b06e3c2e660bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 20:50:08 +0200 Subject: [PATCH 351/431] adding easyconfigs: HMMER2-2.3.2-GCC-8.3.0.eb --- .../h/HMMER2/HMMER2-2.3.2-GCC-8.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-8.3.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-8.3.0.eb new file mode 100644 index 00000000000..07f2dee473f --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' From 4bd3390355ab2881206d69891ded595f10b737de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 20:50:55 +0200 Subject: [PATCH 352/431] adding easyconfigs: antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb --- ...antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb | 84 +++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..a628c3c6bd8 --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'antiSMASH' +version = '5.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/antismash/antismash' +description = """antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary + metabolite biosynthesis gene clusters in bacterial and fungal genomes.""" + +docurls = ['https://docs.antismash.secondarymetabolites.org'] + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('libxml2', '2.9.9'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('DIAMOND', '0.9.30'), + ('FastTree', '2.1.11'), + ('GlimmerHMM', '3.0.4c'), + ('HMMER2', '2.3.2'), + ('HMMER', '3.2.1'), + ('MUSCLE', '3.8.1551'), + ('BLAST+', '2.9.0'), + ('prodigal', '2.6.3'), + ('Biopython', '1.75', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('scikit-learn', '0.21.3', versionsuffix), +] + +# install MEME as a component in this installation, +# since antiSMASH requires very specific old version +# see https://docs.antismash.secondarymetabolites.org/install/#full-manual-install +components = [ + ('MEME', '4.11.2', { + 'source_urls': ['http://meme-suite.org/meme-software/%(version)s/'], + 'sources': ['meme_%(version)s_2.tar.gz'], + 'checksums': ['377238c2a9dda64e01ffae8ecdbc1492c100df9b0f84132d50c1cf2f68921b22'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'meme_%(version)s', + }), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('helperlibs', '0.1.11', { + 'checksums': ['261ddfff1d8f8860198128d51571470dee3a628cc36a2a141c19ce67263b94d3'], + }), + ('pysvg-py3', '0.2.2.post3', { + 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + }), + ('bcbio-gff', '0.6.6', { + 'checksums': ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'], + }), + ('pyScss', '1.3.7', { + 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + }), + (name, version, { + 'source_tmpl': '5-1-2.tar.gz', + 'source_urls': ['https://github.com/antismash/antismash/archive/'], + 'checksums': ['9d20dd865424c3abadd861d977ec8ee3bef3f0a4a4b47cbce46f508c7b891e67'], + }), +] + +sanity_check_paths = { + 'files': ['bin/antismash', 'bin/meme'], + 'dirs': [], +} + +sanity_check_commands = [ + # 'meme -h' exits with non-zero exit status, so use 'grep' to check for pattern + "meme -h 2>&1 | grep 'Usage:[ \t]*meme'", + "antismash --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 0e39bd8d67bfe2e89f9d7b49d68c9de439c5c4ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 May 2020 21:00:03 +0200 Subject: [PATCH 353/431] fix sanity check for extensions in antiSMASH easyconfig + avoid hardcoding dashed version in antiSMASH source spec --- .../a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb index a628c3c6bd8..c882904ce07 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb @@ -54,15 +54,18 @@ exts_list = [ }), ('pysvg-py3', '0.2.2.post3', { 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + 'modulename': 'pysvg', }), ('bcbio-gff', '0.6.6', { 'checksums': ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'], + 'modulename': 'BCBio.GFF' }), ('pyScss', '1.3.7', { 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + 'modulename': 'scss', }), (name, version, { - 'source_tmpl': '5-1-2.tar.gz', + 'source_tmpl': '%s.tar.gz' % '-'.join(version.split('.')), 'source_urls': ['https://github.com/antismash/antismash/archive/'], 'checksums': ['9d20dd865424c3abadd861d977ec8ee3bef3f0a4a4b47cbce46f508c7b891e67'], }), From 35e4ea281ed2b336c33a7b68f00b6f7ed2914368 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 May 2020 08:37:00 +0200 Subject: [PATCH 354/431] also add ggExtra to R 3.6.3 & 4.0.0 --- easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index bbb2c2b8dbf..9d47080b71d 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -2372,6 +2372,15 @@ exts_list = [ ('packrat', '0.5.0', { 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], }), + ('shinyjs', '1.1', { + 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], + }), + ('colourpicker', '1.0', { + 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 6cb1cae0a1c..861f6bb86aa 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2385,6 +2385,15 @@ exts_list = [ ('packrat', '0.5.0', { 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], }), + ('shinyjs', '1.1', { + 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], + }), + ('colourpicker', '1.0', { + 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), ] moduleclass = 'lang' From ce725b6daa858e2a9c3e29153b8fd0a8de02f44d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 May 2020 08:35:23 +0200 Subject: [PATCH 355/431] add ggExtra to R 3.6.2 + FlowSOM to Bioconductor 3.10 bundle --- .../R-bundle-Bioconductor-3.10-foss-2019b.eb | 45 +++++++++++++++++++ .../easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 9 ++++ .../easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 9 ++++ 3 files changed, 63 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb index 739f4d436c3..733edd64e7d 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb @@ -687,6 +687,51 @@ exts_list = [ ('Seurat', '3.1.5', { 'checksums': ['757ef0e7697734aac5769705bef80dc7b95f006cdf52ae7034309a05f11578d1'], }), + ('ALL', '1.28.0', { + 'checksums': ['ef841adc8b366afcdb89de64576ff5ce4cd55ce6c11f5558ada6b074df12d899'], + }), + ('ConsensusClusterPlus', '1.50.0', { + 'checksums': ['e4668aeb05de5e8d836df37bb3bb864e1537c7fdc536d93b31838d66fc2fd05e'], + }), + ('flowViz', '1.50.0', { + 'checksums': ['6792daee4d8a51d5355eec2ba5886971ea89c229050c958dc0e331c7fa326146'], + }), + ('ncdfFlow', '2.32.0', { + 'checksums': ['5100087f9c190c3134a2a3de285de0689d44c43f3283145d04e865024d679a1a'], + }), + ('RProtoBufLib', '1.8.0', { + 'checksums': ['355b5e87d5ffcb0c37bd49a1270e31a876fc0bdd03393620eeeb0c15449c8f36'], + }), + ('flowWorkspace', '3.34.1', { + 'checksums': ['f6423889b403dfbc1ec12dacfc1f21cf6548efab5a808cd9e0194a9abe614bc6'], + }), + ('fda', '5.1.4', { + 'checksums': ['5ddc723dba4019f72c11bab556f5306bdacfa017e7f36bcdc49a4735e87b444b'], + }), + ('flowStats', '3.44.0', { + 'checksums': ['dca4b6e51d14babfec56d969dfaf789acac71245cd9a6ff851d982e42e05145f'], + }), + ('flowClust', '3.24.0', { + 'checksums': ['1a49cb5ecedf2479d052d298039defee517d686ab43cd79cb4221457097b8b4c'], + }), + ('openCyto', '1.24.0', { + 'checksums': ['4b0bde02c853359960186b62eb446339c5fc98e4a5aca7391106ff8037b44540'], + }), + ('isoband', '0.2.1', { + 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], + }), + ('ggplot2', '3.3.0', { + 'checksums': ['320e3c76fe0d0397e29f4782bf85af3647518154b3900a39fd18cf024c554148'], + }), + ('ggcyto', '1.14.1', { + 'checksums': ['a0f00771c4219c2d6de42a7a6d91c507b3123ccb51558e84d236c80aa96e5c9a'], + }), + ('CytoML', '1.12.1', { + 'checksums': ['bfcb1c2f0bd2420bab1df294a6acf056a057b2abaae8dd4bfbfd6ab27846f171'], + }), + ('FlowSOM', '1.18.0', { + 'checksums': ['a56de6acfbb35dd61e4388fa378bd9e98345eaef4962f80a34cdc8fd09d6c508'], + }), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index d3fbe5cd8d1..fd5309d0563 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -2378,6 +2378,15 @@ exts_list = [ ('packrat', '0.5.0', { 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], }), + ('shinyjs', '1.1', { + 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], + }), + ('colourpicker', '1.0', { + 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index d50e89d6e73..7c3815263fe 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -2379,6 +2379,15 @@ exts_list = [ ('packrat', '0.5.0', { 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], }), + ('shinyjs', '1.1', { + 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], + }), + ('colourpicker', '1.0', { + 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), # Specific packages for GPUs ('OpenCL', '0.1-3.1', { 'checksums': ['daff23d777a27cd9d2e67ca8f5db1d29940cf0422708c1ea7e2d9661e3d6ae6f'], From bca1249e59d0ff912cd969851f3b92d02d326f26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 May 2020 11:47:55 +0200 Subject: [PATCH 356/431] add a few more extensions to R 3.6.2 + Bioconductor 3.10 bundle (request by @smoors) --- .../R-bundle-Bioconductor-3.10-foss-2019b.eb | 3 +++ easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 12 ++++++++++++ 3 files changed, 27 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb index 733edd64e7d..73c22b26b0c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb @@ -732,6 +732,9 @@ exts_list = [ ('FlowSOM', '1.18.0', { 'checksums': ['a56de6acfbb35dd61e4388fa378bd9e98345eaef4962f80a34cdc8fd09d6c508'], }), + ('HMMcopy', '1.28.1', { + 'checksums': ['539f4cbd0e558126a5e529beec8fd4b72a42ff04750d34d24b1ea1e40269d02f'], + }), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index fd5309d0563..0810a290d2b 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -2387,6 +2387,18 @@ exts_list = [ ('ggExtra', '0.9', { 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], }), + ('findpython', '1.0.5', { + 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], + }), + ('argparse', '2.0.1', { + 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 7c3815263fe..e7c87a269ca 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -2388,6 +2388,18 @@ exts_list = [ ('ggExtra', '0.9', { 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], }), + ('findpython', '1.0.5', { + 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], + }), + ('argparse', '2.0.1', { + 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), # Specific packages for GPUs ('OpenCL', '0.1-3.1', { 'checksums': ['daff23d777a27cd9d2e67ca8f5db1d29940cf0422708c1ea7e2d9661e3d6ae6f'], From a4370800d1e2fdeab67b4794f1aae173680d4cab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 May 2020 11:49:42 +0200 Subject: [PATCH 357/431] add a few more extensions to R 3.6.3 + 4.0.0 (request by @smoors) --- easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 12 ++++++++++++ 2 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index 9d47080b71d..69b000b9ab3 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -2381,6 +2381,18 @@ exts_list = [ ('ggExtra', '0.9', { 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], }), + ('findpython', '1.0.5', { + 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], + }), + ('argparse', '2.0.1', { + 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 861f6bb86aa..830132ae874 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2394,6 +2394,18 @@ exts_list = [ ('ggExtra', '0.9', { 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], }), + ('findpython', '1.0.5', { + 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], + }), + ('argparse', '2.0.1', { + 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), ] moduleclass = 'lang' From 402fe0133ce75319f7f57c591560c2d9214aa337 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 6 May 2020 16:43:46 +0200 Subject: [PATCH 358/431] Remove download_dep_fail --- .../m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb | 1 - .../m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb index 57c7ba4dbb2..15c988fe00f 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-foss-2019b-Python-3.7.4.eb @@ -18,7 +18,6 @@ dependencies = [ ('networkx', '2.4', versionsuffix), ] -download_dep_fail = True use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb index a4168d99e79..3e34beac879 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-0.20.1-intel-2019b-Python-3.7.4.eb @@ -18,7 +18,6 @@ dependencies = [ ('networkx', '2.4', versionsuffix), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 5495e28d23898d7c39a8933ac7c6617d8ab84d71 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 May 2020 18:05:34 +0200 Subject: [PATCH 359/431] adding easyconfigs: MEM-20191023-foss-2019b-R-3.6.2.eb --- .../m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb diff --git a/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb b/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb new file mode 100644 index 00000000000..9c584099de7 --- /dev/null +++ b/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'MEM' +local_commit = '6b92476' +version = '20191023' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cytolab/mem' +description = "Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores." + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/cytolab/mem/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['735cc340fb644ddc4bd760d6897d3911561ea4735db10e799ff34e36ba138a86'] + +dependencies = [ + ('R', '3.6.2'), + ('R-bundle-Bioconductor', '3.10'), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'tools' From 2fb6f5a94ddf0b052e555eea25a08699e54b53a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 6 May 2020 20:40:58 +0200 Subject: [PATCH 360/431] Archive old Singularity configs --- .../s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb | 0 .../s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb | 0 .../s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb | 0 .../s/Singularity/Singularity-2.4.2-GCC-5.4.0-2.26.eb | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/s/Singularity/Singularity-2.4.2-GCC-5.4.0-2.26.eb (100%) diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/__archive__/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb similarity index 100% rename from easybuild/easyconfigs/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb rename to easybuild/easyconfigs/__archive__/s/Singularity/Singularity-1.0-GCC-4.9.3-2.25.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/__archive__/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb similarity index 100% rename from easybuild/easyconfigs/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb rename to easybuild/easyconfigs/__archive__/s/Singularity/Singularity-2.2.1-GCC-6.3.0-2.27.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/__archive__/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb similarity index 100% rename from easybuild/easyconfigs/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/__archive__/s/Singularity/Singularity-2.3.1-GCC-5.4.0-2.26.eb diff --git a/easybuild/easyconfigs/s/Singularity/Singularity-2.4.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/__archive__/s/Singularity/Singularity-2.4.2-GCC-5.4.0-2.26.eb similarity index 100% rename from easybuild/easyconfigs/s/Singularity/Singularity-2.4.2-GCC-5.4.0-2.26.eb rename to easybuild/easyconfigs/__archive__/s/Singularity/Singularity-2.4.2-GCC-5.4.0-2.26.eb From a8f3b3a9c79611a1708cf0f788f25be8797927b5 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 6 May 2020 19:05:42 +0000 Subject: [PATCH 361/431] Fix building [foss/2019b] ITK v5.0.1 (locale & libjpeg) --- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 39bc4f30c61..b4ba37f337b 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -51,7 +51,7 @@ configopts = '-DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING= configopts += '-DITK_WRAP_PYTHON=ON -DITK_LEGACY_SILENT=ON ' configopts += '-DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_EIGEN=ON -DITK_USE_SYSTEM_HDF5=ON ' configopts += '-DITK_USE_SYSTEM_JPEG=ON -DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' -configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib*/libjpeg.%s ' % SHLIB_EXT configopts += '-DITK_USE_SYSTEM_PNG=ON -DPNG_PNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT configopts += '-DITK_USE_SYSTEM_TIFF=ON -DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' @@ -60,6 +60,7 @@ configopts += '-DITK_USE_SYSTEM_ZLIB=ON -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +prebuildopts = "env LC_ALL=C " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " sanity_check_paths = { From e4dd2b8347757362bf9d050ac1fb62dd6af2625d Mon Sep 17 00:00:00 2001 From: crubb Date: Thu, 7 May 2020 09:41:08 +0200 Subject: [PATCH 362/431] Update easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb Co-authored-by: Alexander Grund --- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index b4ba37f337b..4ecc1f13527 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -60,7 +60,7 @@ configopts += '-DITK_USE_SYSTEM_ZLIB=ON -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' -prebuildopts = "env LC_ALL=C " +prebuildopts = "LC_ALL=C " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " sanity_check_paths = { From 221059147a2d4bb149785def49fe33b18ade7102 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 7 May 2020 12:22:26 +0200 Subject: [PATCH 363/431] adding easyconfigs: CaSpER-2.0-foss-2019b.eb --- .../c/CaSpER/CaSpER-2.0-foss-2019b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CaSpER/CaSpER-2.0-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/CaSpER/CaSpER-2.0-foss-2019b.eb b/easybuild/easyconfigs/c/CaSpER/CaSpER-2.0-foss-2019b.eb new file mode 100644 index 00000000000..377a3f60ae3 --- /dev/null +++ b/easybuild/easyconfigs/c/CaSpER/CaSpER-2.0-foss-2019b.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'CaSpER' +version = '2.0' +local_biocver = '3.10' +github_account = 'akdess' + +homepage = 'https://github.com/akdess/CaSpER' +description = """ CaSpER is a signal processing approach for identification, visualization, and integrative analysis + of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data. """ + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4573d614d7107a798b5f733e65b7addb51359068fb368e3873d1adc96229fa3e'] + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('R', '3.6.2'), + ('R-bundle-Bioconductor', local_biocver), +] + +# remove pre-existing object files before compiling +installopts = '--preclean' + +sanity_check_paths = { + 'files': [], + 'dirs': ['CaSpER'], +} + +moduleclass = 'bio' From cb32628d77c509c0cbd9d498e481cc2f5ed68c7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2020 13:52:32 +0200 Subject: [PATCH 364/431] add diffcyt extension to R-bundle-Bioconductor 3.10 --- .../R-bundle-Bioconductor-3.10-foss-2019b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb index 73c22b26b0c..2cd65bfa5a7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.10-foss-2019b.eb @@ -735,6 +735,9 @@ exts_list = [ ('HMMcopy', '1.28.1', { 'checksums': ['539f4cbd0e558126a5e529beec8fd4b72a42ff04750d34d24b1ea1e40269d02f'], }), + ('diffcyt', '1.6.6', { + 'checksums': ['7bb7203b399c0d96920c80d2e027003ba584e06d02a8261d6e300724e9278ed6'], + }), ] modextrapaths = {'R_LIBS': ''} From 5aa9f94bb87ec4934d9203e61897ba0c2e576efd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2020 18:12:33 +0200 Subject: [PATCH 365/431] adding easyconfigs: MESS-0.1.6-foss-2019b.eb, SLATEC-4.1-GCC-8.3.0.eb --- .../m/MESS/MESS-0.1.6-foss-2019b.eb | 55 +++++++++++++++++++ .../s/SLATEC/SLATEC-4.1-GCC-8.3.0.eb | 36 ++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb create mode 100644 easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb b/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb new file mode 100644 index 00000000000..8990da288b1 --- /dev/null +++ b/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb @@ -0,0 +1,55 @@ +easyblock = 'Bundle' + +name = 'MESS' +# see meta.yaml for corresponding version +local_commit = '2e98ff3debfe7cc21eb360000124641d78c4b03e' +version = '0.1.6' + +homepage = 'https://github.com/PACChem/MESS' +description = "Master Equation System Solver (MESS)" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/PACChem/MESS/archive/'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [('SLATEC', '4.1')] + +components = [ + # MPACK includes old copies of GMP/MPFR/MPC, + # providing those as proper dependencies is not an option (due to API changes in recent versions) + ('MPACK', 'included', { + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'MESS-%s.tar.gz' % version}], + 'checksums': ['d09d71f52771ac945f4898c6d000bca00798c406772432a8993e0b24de526c43'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'MESS-%s/external/MPACK' % local_commit, + 'preconfigopts': 'export BLAS_LIBS="$LIBBLAS" && export LAPACK_LIBS="$LIBLAPACK" && ', + # MPACK code is quite old, need -std=c++98 to avoid errors like 'lvalue required as left operand of assignment' + 'buildopts': 'CXXFLAGS="$CXXFLAGS -std=c++98"', + }), + (name, version, { + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d09d71f52771ac945f4898c6d000bca00798c406772432a8993e0b24de526c43'], + 'easyblock': 'CMakeMake', + 'start_dir': 'MESS-%s' % local_commit, + 'configopts': "-DCMAKE_EXE_LINKER_FLAGS='-lgfortran'", + }), +] + +local_libs = ['gmp', 'mblas_dd', 'mblas_dd_ref', 'mblas_double', 'mblas_double_ref', 'mblas_gmp', 'mblas_gmp_ref', + 'mblas_mpfr', 'mblas_mpfr_ref', 'mblas_qd', 'mblas_qd_ref', 'mlapack_dd', 'mlapack_dd_ref', + 'mlapack_double', 'mlapack_double_ref', 'mlapack_gmp', 'mlapack_gmp_ref', 'mlapack_mpfr', + 'mlapack_mpfr_ref', 'mlapack_qd', 'mlapack_qd_ref', 'mpfr', 'mpc', 'qd'] + +sanity_check_paths = { + 'files': ['bin/mess', 'bin/messabs', 'bin/messpf', 'bin/messsym'] + ['lib/lib%s.a' % l for l in local_libs] + + # no libqd.so, only libqd.a + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in local_libs if l != 'qd'], + 'dirs': ['include/qd'], +} + +# running without arguments prints usage and exits with 0 +sanity_check_commands = ["mess"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCC-8.3.0.eb b/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCC-8.3.0.eb new file mode 100644 index 00000000000..bfbbfc1059e --- /dev/null +++ b/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCC-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'SLATEC' +version = '4.1' + +homepage = 'https://www.netlib.org/slatec/' +description = """SLATEC Common Mathematical Library, a comprehensive software library containing + over 1400 general purpose mathematical and statistical routines written in Fortran 77.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +sources = [{ + 'source_urls': ['https://www.netlib.org/%(namelower)s'], + 'filename': '%(namelower)s_src.tgz', + 'extract_cmd': 'tar xfvz %s', +}, { + 'source_urls': ['http://www.netlib.org/%(namelower)s'], + 'filename': '%(namelower)s4linux.tgz', + 'extract_cmd': 'tar xfvz %s -C src', +}] +checksums = [ + 'df009d9ef9c18aae06ce68711b1ae108d3533b4f174582c3cbea0915c4fdfe01', # slatec_src.tgz + 'eef9234f8fcb49e7f4905a11eda8f453ec2ca314029a9ce303fdbc99cff42bf3', # slatec4linux.tgz +] + +skipsteps = ['configure'] + +preinstallopts = "sed -i 's+/usr/local+%(installdir)s+; s+ldconfig;++' makefile &&" +preinstallopts += "mkdir -p %(installdir)s/lib %(installdir)s/man/man1 &&" + +sanity_check_paths = { + 'files': ['lib/libslatec.a', 'lib/libslatec.%s' % SHLIB_EXT], + 'dirs': ['lib', 'man/man1'] +} + +moduleclass = 'math' From e55bead13baf4271a6f81b92fb4ecde7433a0662 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2020 18:36:18 +0200 Subject: [PATCH 366/431] fix style issue in MESS easyconfig --- easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb b/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb index 8990da288b1..da3cab372a9 100644 --- a/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb +++ b/easybuild/easyconfigs/m/MESS/MESS-0.1.6-foss-2019b.eb @@ -44,8 +44,7 @@ local_libs = ['gmp', 'mblas_dd', 'mblas_dd_ref', 'mblas_double', 'mblas_double_r sanity_check_paths = { 'files': ['bin/mess', 'bin/messabs', 'bin/messpf', 'bin/messsym'] + ['lib/lib%s.a' % l for l in local_libs] + - # no libqd.so, only libqd.a - ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in local_libs if l != 'qd'], + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in local_libs if l != 'qd'], # no libqd.so, only libqd.a 'dirs': ['include/qd'], } From 6accfac2548ec9d80a67037ddd647a4286669f37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 May 2020 20:01:59 +0200 Subject: [PATCH 367/431] get rid of -R-* versionsuffix for MEM + leave extending $R_LIBS to RPackage easyblock --- ...191023-foss-2019b-R-3.6.2.eb => MEM-20191023-foss-2019b.eb} | 3 --- 1 file changed, 3 deletions(-) rename easybuild/easyconfigs/m/MEM/{MEM-20191023-foss-2019b-R-3.6.2.eb => MEM-20191023-foss-2019b.eb} (91%) diff --git a/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb b/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b.eb similarity index 91% rename from easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb rename to easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b.eb index 9c584099de7..78f35cd7b56 100644 --- a/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b-R-3.6.2.eb +++ b/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'RPackage' name = 'MEM' local_commit = '6b92476' version = '20191023' -versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/cytolab/mem' description = "Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores." @@ -19,8 +18,6 @@ dependencies = [ ('R-bundle-Bioconductor', '3.10'), ] -modextrapaths = {'R_LIBS': ''} - sanity_check_paths = { 'files': [], 'dirs': [name], From 107246ee4f2bfd6819a8c6292f1c7174420b2bb5 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 7 May 2020 20:38:10 +0000 Subject: [PATCH 368/431] adding easyconfigs: nifti2dicom-0.4.11-foss-2019b.eb, TCLAP-1.2.2-GCCcore-8.3.0.eb and patches: nifti2dicom-0.4.11-no_GUI.patch --- .../nifti2dicom-0.4.11-foss-2019b.eb | 38 ++++++++ .../nifti2dicom-0.4.11-no_GUI.patch | 89 +++++++++++++++++++ .../t/TCLAP/TCLAP-1.2.2-GCCcore-8.3.0.eb | 26 ++++++ 3 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb create mode 100644 easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-no_GUI.patch create mode 100644 easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.2-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb b/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb new file mode 100644 index 00000000000..4f4ab7d6a83 --- /dev/null +++ b/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'nifti2dicom' +version = '0.4.11' + +homepage = 'https://github.com/biolab-unige/nifti2dicom' +description = """Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, +including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that +is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM +tags, in order to create a valid DICOM that can be imported in a PACS.""" + + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/biolab-unige/nifti2dicom/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['nifti2dicom-%(version)s-no_GUI.patch'] +checksums = [ + 'df8dc81797227bb4b1ca8f4e52abf10350c4cdd7bc82e4b0a0c59cb4f879f0d4', # v0.4.11.tar.gz + '848aace88cd9bbd7a912717453faf060cf2e5c7e95394a9260c4a3d54f127527', # nifti2dicom-0.4.11-no_GUI.patch +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +dependencies = [ + ('ITK', '5.0.1', '-Python-3.7.4'), + ('TCLAP', '1.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/nifti2dicom'], + 'dirs': ['share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-no_GUI.patch b/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-no_GUI.patch new file mode 100644 index 00000000000..420b6d2750f --- /dev/null +++ b/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-no_GUI.patch @@ -0,0 +1,89 @@ +This patch removes the build targets for the Qt based GUI and docs (VTK is therefore not needed anymore, either), +which had reproducable trouble builing and would require quite a number of nowadays obsolete dependencies. + +Author: https://github.com/crubb + +diff -ur nifti2dicom-0.4.11/CMakeLists.txt nifti2dicom-0.4.11-noGUI/CMakeLists.txt +--- nifti2dicom-0.4.11/CMakeLists.txt 2016-03-01 13:28:06.000000000 +0000 ++++ nifti2dicom-0.4.11-noGUI/CMakeLists.txt 2018-08-24 07:04:27.124996116 +0000 +@@ -45,22 +45,6 @@ + find_package(VTK REQUIRED) + include(${VTK_USE_FILE}) + +-#TODO Check QVTK +- +-if(VTK_QT_VERSION EQUAL 5) +- set(Nifti2Dicom_QT_VERSION 5) +- +- #Check Qt5 Library [Qt5] +- find_package(Qt5 COMPONENTS Core Gui Widgets) +-else() +- set(Nifti2Dicom_QT_VERSION 4) +- +- #Check Qt4 Library [Qt4] (4.4.0) +- set(QT_USE_IMPORTED_TARGETS TRUE) +- find_package(Qt4 4.4.0 REQUIRED) +- +-endif() +- + + configure_file(${CMAKE_SOURCE_DIR}/Nifti2DicomConfig.h.cmake ${CMAKE_BINARY_DIR}/Nifti2DicomConfig.h) + +@@ -94,6 +78,5 @@ + + + add_subdirectory(src) +-add_subdirectory(doc) + add_subdirectory(data) + add_subdirectory(packaging) +diff -ur nifti2dicom-0.4.11/doc/CMakeLists.txt nifti2dicom-0.4.11-noGUI/doc/CMakeLists.txt +--- nifti2dicom-0.4.11/doc/CMakeLists.txt 2016-03-01 13:28:06.000000000 +0000 ++++ nifti2dicom-0.4.11-noGUI/doc/CMakeLists.txt 2018-08-24 06:58:20.798065098 +0000 +@@ -56,18 +56,7 @@ + --output=${CMAKE_CURRENT_SOURCE_DIR}/man/man1/nifti2dicom.1 + COMMAND ${SED_EXECUTABLE} -i "s#${CMAKE_BINARY_DIR}/src/core/##g" ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/nifti2dicom.1 + ) +- add_custom_command(OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/qnifti2dicom.1 +- DEPENDS qnifti2dicom ${CMAKE_CURRENT_SOURCE_DIR}/man/qnifti2dicom.help2man.include +- COMMAND ${HELP2MAN_EXECUTABLE} +- ${CMAKE_BINARY_DIR}/src/gui/qnifti2dicom +- --version-string=${Nifti2Dicom_VERSION} +- --no-info +- --include=${CMAKE_CURRENT_SOURCE_DIR}/man/qnifti2dicom.help2man.include +- --output=${CMAKE_CURRENT_SOURCE_DIR}/man/man1/qnifti2dicom.1 +- COMMAND ${SED_EXECUTABLE} -i "s#${CMAKE_BINARY_DIR}/src/gui/##g" ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/qnifti2dicom.1 +- ) + add_custom_target(regenerate_man SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/nifti2dicom.1 +- ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/qnifti2dicom.1 + ) + endif(ENABLE_REGENERATE_MAN) + +@@ -80,19 +69,10 @@ + COMMAND ${GZIP_EXECUTABLE} -9 -f -n ${CMAKE_CURRENT_BINARY_DIR}/man/man1/nifti2dicom.1 + DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/nifti2dicom.1 + ) +- add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/man/man1/qnifti2dicom.1.gz +- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/qnifti2dicom.1 ${CMAKE_CURRENT_BINARY_DIR}/man/man1/qnifti2dicom.1 +- COMMAND ${GZIP_EXECUTABLE} -9 -f -n ${CMAKE_CURRENT_BINARY_DIR}/man/man1/qnifti2dicom.1 +- DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/man/man1/qnifti2dicom.1 +- ) + +- add_custom_target(manpages ALL SOURCES ${CMAKE_CURRENT_BINARY_DIR}/man/man1/nifti2dicom.1.gz +- ${CMAKE_CURRENT_BINARY_DIR}/man/man1/qnifti2dicom.1.gz) ++ add_custom_target(manpages ALL SOURCES ${CMAKE_CURRENT_BINARY_DIR}/man/man1/nifti2dicom.1.gz) + + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/man/man1/nifti2dicom.1.gz + DESTINATION share/man/man1 + COMPONENT Documentation) +- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/man/man1/qnifti2dicom.1.gz +- DESTINATION share/man/man1 +- COMPONENT Documentation) + endif() +diff -ur nifti2dicom-0.4.11/src/CMakeLists.txt nifti2dicom-0.4.11-noGUI/src/CMakeLists.txt +--- nifti2dicom-0.4.11/src/CMakeLists.txt 2016-03-01 13:28:06.000000000 +0000 ++++ nifti2dicom-0.4.11-noGUI/src/CMakeLists.txt 2018-08-24 06:32:21.374915832 +0000 +@@ -18,4 +18,3 @@ + + + add_subdirectory(core) +-add_subdirectory(gui) diff --git a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..f294e30162d --- /dev/null +++ b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.2-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'TCLAP' +version = '1.2.2' + +homepage = 'http://tclap.sourceforge.net/' +description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing +command line arguments. It was intially inspired by the user friendly CLAP libary.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f5013be7fcaafc69ba0ce2d1710f693f61e9c336b6292ae4f57554f59fde5837'] + +builddependencies = [ + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['include/tclap/CmdLine.h'], + 'dirs': [''], +} + +moduleclass = 'lib' From 46c21a6afa3c4e04953fe05f814018b4304053e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 May 2020 09:56:43 +0200 Subject: [PATCH 369/431] {bio}[foss/2020a] R-bundle-Bioconductor v3.11 --- ...MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb | 34 + .../n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb | 29 + ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 778 ++++++++++++++++++ 3 files changed, 841 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..65b1182cd02 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.1.7-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB-connector-c' +version = '3.1.7' + +homepage = 'https://downloads.mariadb.org/connector-c/' +description = "MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/MariaDB/mariadb-connector-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6bda309fd71aa01e5d32c48768cb4fb5abcb760b1272e270901f4e47cd759d6'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +# don't use gold linker, leads to error: "invalid use of VERSION in input file" +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd'" + +sanity_check_paths = { + 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT], + 'dirs': ['include/mariadb'], +} + +modextrapaths = { + 'CPATH': ['include/mariadb'], + 'LD_LIBRARY_PATH': ['lib/mariadb'], + 'LIBRARY_PATH': ['lib/mariadb'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..d10dda330a5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2020a-R-4.0.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.17' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = "ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'] + +dependencies = [ + ('R', '4.0.0'), + ('netCDF', '4.7.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..024bac5a9a2 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -0,0 +1,778 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.11' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('R', '4.0.0'), + ('HDF5', '1.10.6'), # for rhdf5 + ('MariaDB-connector-c', '3.1.7'), # for RMySQL + ('ncdf4', '1.17', versionsuffix), # for mzR +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.11/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.11/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on May 7th 2020 +exts_list = [ + ('readr', '1.3.1', { + 'checksums': ['33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3'], + }), + ('BiocGenerics', '0.34.0', { + 'checksums': ['534f5640fe0f1c165f164ebb26e312c4140e336145af3c839dbff427a0c7db96'], + }), + ('Biobase', '2.48.0', { + 'checksums': ['17dbdfd9f06a7dcca5daeb067a7acf46391f155c3321e119b20b9edaed9be38e'], + }), + ('S4Vectors', '0.26.0', { + 'checksums': ['757aaf89c177a228a0c418c1f141fffc587e115a8e6d4259bada7341a7c9131e'], + }), + ('IRanges', '2.22.1', { + 'checksums': ['72b531e0c69c584525e3812be40e7c3dcc84a30461a42be5832c859b7b49d9e5'], + }), + ('GenomeInfoDbData', '1.2.3', { + 'checksums': ['945d79fc542ce7914fc89ad95bd0ead827597cfa50f2f758cfef42a09fc78aeb'], + }), + ('GenomeInfoDb', '1.24.0', { + 'checksums': ['3be2fabf1946a16bd4d4d818c34e58c0af0b6f8c108b50ee831b6e7ab0156929'], + }), + ('AnnotationDbi', '1.50.0', { + 'checksums': ['05dca3e4bb1c3a6e3584707f58692138d518a189607f958465f0624055a7f781'], + }), + ('zlibbioc', '1.34.0', { + 'checksums': ['8026a46a06bf951481fe2281261c714f6996989dfc77176d609c892545013448'], + }), + ('XVector', '0.28.0', { + 'checksums': ['6cdf01943177f9aeba808b028ad3261d2bba91fb26a3be5ec0281db2bf860186'], + }), + ('Biostrings', '2.56.0', { + 'checksums': ['286e06883c4c230b696e89b06fba78ba418db15559def871a163a1d7ce77b046'], + }), + ('GenomicRanges', '1.40.0', { + 'checksums': ['a18bb9cddf7a147b8c8b53f0f024a3ed77637f7c54452e7eda37038c45fec172'], + }), + ('BiocParallel', '1.22.0', { + 'checksums': ['4fa0a5f777de5c9cda96cfe2e93cd34f2686df84bf4507cc2c9e0e596a2f4fd3'], + }), + ('Rhtslib', '1.20.0', { + 'checksums': ['b13d3f20f483dedc778d1a386ce1d1fe394ddbb9710c4b588836ff99593cd9a0'], + }), + ('Rsamtools', '2.4.0', { + 'checksums': ['78039e3781865d79af36bd4bd3926148e8bb94b78668abcf0c24b97034f8017c'], + }), + ('DelayedArray', '0.14.0', { + 'checksums': ['1307d776d52d837b77b9bd490bb4a3e7a7c12f9a751c6009e1633b9a3350e7d3'], + }), + ('SummarizedExperiment', '1.18.1', { + 'checksums': ['4cb0e16e9ac4506e3141ce8fe0a67b2c29555272b1ebdd88b30ddc56663a2c1f'], + }), + ('GenomicAlignments', '1.24.0', { + 'checksums': ['0dcded5d0ca3d79a3fa1f0836e23f94b25ced099f193591922b7d4ec4e33136d'], + }), + ('ShortRead', '1.46.0', { + 'checksums': ['6d804cc5dc780935c83580584a1f93ae80d76f9562c70e2c85def8642c6d9350'], + }), + ('graph', '1.66.0', { + 'checksums': ['2f59e997e45d138c3de3a640fb698eba3a8c7cd081465a6cab5fdfff52b76097'], + }), + ('affyio', '1.58.0', { + 'checksums': ['b89c65471b1d331c163f9ab13130cd65f476aaabeadf8c678506fb0448302e48'], + }), + ('preprocessCore', '1.50.0', { + 'installopts': "--configure-args='--disable-threading'", + 'checksums': ['54f2d594b9927d30a076f3bd10e1faee9271c9689e8f59ec478c7aaea7012460'], + }), + ('BiocManager', '1.30.10', { + 'checksums': ['f3b7a412b42be0ab8df5fcd9bf981876ba9e5c55bc5faaca7af7ede3b6d0c90e'], + }), + ('affy', '1.66.0', { + 'checksums': ['ccdf60e2d40d324be759d389b4cdfeac6b66c44c9043ab8605c8e9daa59fd054'], + }), + ('GO.db', '3.11.1', { + 'checksums': ['105ca31adb7ea5d2327d319e64bd024d098da36cc49fa214b13ef402e9756acb'], + }), + ('limma', '3.44.1', { + 'checksums': 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['db6d5fd3a77ac9473bf21f84b65da3c6e485f9ed33f5313bbf0ec852b71db97e'], + }), + ('Rfast', '1.9.9', { + 'checksums': ['c0932398a4783a33586d5cc47b79592cd2b8220cb76d7530e4cf4f221eeca8a2'], + }), + ('ChIPpeakAnno', '3.22.0', { + 'checksums': ['980389b98b05b5b88337e41fafb23207a33fc8fafc5be14bccf8852d398f391b'], + }), + ('seqLogo', '1.54.1', { + 'checksums': ['61cc237ad648c86be451450d2128120dcec969b4b1e574e0730d233307ab1c57'], + }), + ('rGADEM', '2.36.0', { + 'checksums': ['e86b6271cb57f63db101c3bb21321061dddab96c9ab65fc01a2e4908f9a2ae92'], + }), + ('MotIV', '1.43.0', { + 'checksums': ['06d2884741f79b29b1fa1a53dcc57842a41476a41e203ea0d997729b59f518fb'], + }), + ('MotifDb', '1.30.0', { + 'checksums': ['752ea5904f4e37594a555c24a4d0a43f6bbd568e5cd882b24abb030d2e6eb547'], + }), + ('motifStack', '1.32.0', { + 'checksums': ['45d3d1bd4527729c2dc1f93d0947ba54f8be39be8dea4c23413f7acf64150e01'], + }), + ('ATACseqQC', '1.12.0', { + 'checksums': ['e75a11b1559af0e0c153396652aa6b69740b6cfa0052a7a1f73a02a5b940d294'], + }), + ('batchelor', '1.4.0', { + 'checksums': ['913eb386120cb8fb6ca500a91b59918d5c8ba76ef403f749c69d668687558885'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.52.0', { + 'checksums': ['c9bf40f67a0c23e18d48b968ca285bc844ca5108f6e8f963bf9b41e5f638ed83'], + }), + ('R.devices', '2.16.1', { + 'checksums': ['adedb928e6e6d1951d512f13688aa8ad4558a8fbc5b3e58cc0901ff106b6f497'], + }), + ('R.filesets', '2.13.0', { + 'checksums': ['cf1597227bc2cc4b3f4a2bdf087e1ed33330a8450655d6a72236d105f0f39988'], + }), + ('aroma.light', '3.18.0', { + 'checksums': ['ccb305b421b10425b9a59c213a9fef6a5e3e71d883c0f6c7b957741bab70c5a7'], + }), + ('PSCBS', '0.65.0', { + 'checksums': ['3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a'], + }), + ('aroma.core', '3.2.1', { + 'checksums': ['2f815d4a0b2e0fec89006e6a07e1322cd6df529f725b22fd7f4b49380f4488d9'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('R.utils', '2.9.2', { + 'checksums': ['ac6b3b8e814fbb855c38fbdb89a4f0cf0ed65ce7fa308445bd74107fbc0d32cf'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('Repitools', '1.34.0', { + 'checksums': ['4580abf755bef3e16c60a04debace613ee8cffafc6d3001d14743b6b4465d586'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.3', { + 'checksums': ['c29911ca93935e3b9aa6a67e894337dc2ad707405da1500c9898bd0578519ecc'], + }), + ('MEDIPS', '1.40.0', { + 'checksums': ['08edf0812c4c419bcf51c586773dd6d5495e09b6d03a6e10539ded6ad5f2c293'], + }), + ('RProtoBufLib', '2.0.0', { + 'checksums': ['fa6e04f9196fa0df55f4a886d8f00ef99d525a140371553b2e31b0bf93b3d14d'], + }), + ('cytolib', '2.0.0', { + 'checksums': ['5b5ff0a82cc09c255ad5c3a2a0c9ad81c12e2106412292c499b9207c7c2d482d'], + }), + ('flowCore', '2.0.0', { + 'checksums': ['832b9bdbc89549c6084814150a5fa197869aff1e8c9f9573811394172ad588bb'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('metap', '1.3', { + 'checksums': ['7fcf148bfd77f445b2ee68cbd2367caaf991028d9843020c755dd11965adb5ca'], + }), + ('uwot', '0.1.8', { + 'checksums': ['ede6e061b43f9e1337c0132a5334082f4565ec1623bbb0eee1f738034346f0cb'], + }), + ('Seurat', '3.1.5', { + 'checksums': ['757ef0e7697734aac5769705bef80dc7b95f006cdf52ae7034309a05f11578d1'], + }), + ('ALL', '1.29.0', { + 'checksums': ['6e8d543de21ee98c00f487902077c55e8e8509bc3f09563dd09549807bfff6d8'], + }), + ('ConsensusClusterPlus', '1.52.0', { + 'checksums': ['98fddf86255dc641beb3ccd8fd9b1c8ace430146ea87be3e0c750258921af819'], + }), + ('flowViz', '1.52.0', { + 'checksums': ['d883feadc65cae7d3bc44d59b366a249b05b5f99749d71e8cb3c61551b777238'], + }), + ('ncdfFlow', '2.34.0', { + 'checksums': ['2ec9c135940c8d0f300ac353504705a9edf7b93cbf6766e70bd311b894b07d2b'], + }), + ('RProtoBufLib', '2.0.0', { + 'checksums': ['fa6e04f9196fa0df55f4a886d8f00ef99d525a140371553b2e31b0bf93b3d14d'], + }), + ('flowWorkspace', '4.0.0', { + 'checksums': ['a06ca759ba998ad2287183eca8f6cba99889e32a44caf4a39a9680c56b7c110e'], + }), + ('fda', '5.1.4', { + 'checksums': ['5ddc723dba4019f72c11bab556f5306bdacfa017e7f36bcdc49a4735e87b444b'], + }), + ('flowStats', '4.0.0', { + 'checksums': ['39b69ff7248f3832ad018f206e02642ef0cd1bf37040e00f48571a7fdaeefbf9'], + }), + ('flowClust', '3.26.0', { + 'checksums': ['abe01b47e7692f335b5f0418cef6dd0dbf99df871bda49fa015dc9407cc2b31a'], + }), + ('openCyto', '2.0.0', { + 'checksums': ['3521a9d76414f35060a0fb39a0e688695db41ad6cbf10b37387bead69a69be81'], + }), + ('isoband', '0.2.1', { + 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], + }), + ('ggplot2', '3.3.0', { + 'checksums': ['320e3c76fe0d0397e29f4782bf85af3647518154b3900a39fd18cf024c554148'], + }), + ('ggcyto', '1.16.0', { + 'checksums': ['e012f204a01c6b3427a5b29050e37c8034f44a9a5a30ba50b75dcae3d57b06c6'], + }), + ('CytoML', '2.0.0', { + 'checksums': ['38804bfff42ef82db35022eb16cd01e34a8ce8d5840b3983a6b4c4e48914f87e'], + }), + ('FlowSOM', '1.20.0', { + 'checksums': ['e84069bef95e4b748e64171fac38ea99dfbfd982c9cb2b0f616cb580c99627dc'], + }), + ('HMMcopy', '1.30.0', { + 'checksums': ['94513a4a3398e8526cdd3d77a5525380d3dcdcab6c996b0d68a88d262d9fffdc'], + }), + ('diffcyt', '1.8.0', { + 'checksums': ['4bef82e672959efa88b124d5c6d73b02e06f1af8f9cfc52c29a269824daac8e7'], + }), + ('blme', '1.0-4', { + 'checksums': ['c2bfc6b7804cdc1f1b95cd6ce215a13a7c7aa5833ad9cfe8900e4c44045842b1'], + }), + ('colorRamps', '2.3', { + 'checksums': ['3f10eab0602a42a2e5a79c7c04638be06cbf1e6f23979a1bd95d853e10940b6a'], + }), + ('variancePartition', '1.18.0', { + 'checksums': ['b589a1479b314374cfcc448ad6254a047d07853f3690d6c25c50b7837129c6e6'], + }), + ('muscat', '1.2.0', { + 'checksums': ['83c4a88e1cd87fcbe5395655fe02a07f9d00f211a46d547b11543d993436e1f7'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 44313dfa801beb6a20415bdc3a40c0248cd68340 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 8 May 2020 10:04:00 +0200 Subject: [PATCH 370/431] adding easyconfigs: TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb --- ...rFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb | 144 ++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..95d9b76fa77 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [ + ('Bazel', '2.0.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + # For SciPy + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('cuDNN', '7.6.4.38'), + ('NCCL', '2.4.8'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +exts_list = [ + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('pyasn1-modules', '0.2.8', { + 'modulename': 'pyasn1_modules', + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.0', { + 'checksums': ['1a836406405730121ae9823e19c6e806c62bbad73f890574fff50efa4122c487'], + }), + ('cachetools', '4.1.0', { + 'checksums': ['1d057645db16ca7fe1f3bd953558897603d6f0b9c51ed9d11eb4d071ec4e2aab'], + }), + ('google-auth', '1.14.2', { + 'modulename': 'google.auth', + 'checksums': ['2243db98475f7f2033c41af5185333cbf13780e8f5f96eaadd997c6f34181dcc'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'modulename': 'requests_oauthlib', + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.1', { + 'modulename': 'google_auth_oauthlib', + 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('protobuf', '3.11.3', { + 'modulename': 'google.protobuf', + 'checksums': ['c77c974d1dadf246d789f6dad1c24426137c9091e930dbf50e0a29c1fcf00b1f'], + }), + ('absl-py', '0.9.0', { + 'modulename': 'absl', + 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.28.1', { + 'modulename': 'grpc', + 'checksums': ['cbc322c5d5615e67c2a15be631f64e6c2bab8c12505bc7c150948abdaa0bdbac'], + }), + ('tensorboard-plugin-wit', '1.6.0.post3', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['1fdf4ac343f1665453205aef8bb227b0204893bb5ffb792d2ed4509b1daf3d4f'], + }), + ('tensorboard', '2.2.1', { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['9a2a2dc9856187679e93f3c95e5dc771dd47e3257db09767b4be118d734b4dc2'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.2.1', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['83b76a98d18ae6a5cc7a0d88955a7f74881f0e567a0f4c949d24c942753eb998'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.0', { + 'modulename': 'keras_preprocessing', + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-1.14.0_swig-env.patch', + 'TensorFlow-1.14.0_remove_usrbin_from_linker_bin_path_flag.patch', + 'TensorFlow-2.1.0_fix-cuda-build.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + '69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3', # v2.2.0.tar.gz + 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', # TensorFlow-1.14.0_swig-env.patch + # TensorFlow-1.14.0_remove_usrbin_from_linker_bin_path_flag.patch + 'bfa2701495dddfbbf4fbec808ea3c982b50043a16d28a8d1283f44df0b8aae7d', + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + ], + }), +] + +moduleclass = 'lib' From 3a7959c38350d745bca0e7acd412d2034b0c9dd9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 8 May 2020 10:20:35 +0200 Subject: [PATCH 371/431] Add Bazel dependency --- .../b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..106e2146849 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb @@ -0,0 +1,25 @@ +name = 'Bazel' +version = '2.0.0' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['Bazel-0.29.1_fix-gold-flag.patch'] +checksums = [ + '724da3c656f68e787a86ebb9844773aa1c2e3a873cc39462a8f1b336153d6cbb', # bazel-2.0.0-dist.zip + '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch +] + +builddependencies = [ + ('binutils', '2.32'), + ('Python', '3.7.4'), + ('Zip', '3.0'), +] +dependencies = [('Java', '1.8', '', True)] + +moduleclass = 'devel' From 7f2aed4d9883399734b59e9da739696d25731c55 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 8 May 2020 10:39:19 +0200 Subject: [PATCH 372/431] adding easyconfigs: minimap2-2.17-GCCcore-9.3.0.eb --- .../m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..99066113b93 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.17' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] + +builddependencies = [('binutils', '2.34')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +moduleclass = 'bio' From cdbc0c399524635c095d4c82bdb439365be059fb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 8 May 2020 11:00:19 +0200 Subject: [PATCH 373/431] move sanity_check_commands and wolframscript fix to the easyblock --- easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb index 73b83549ef7..2f5ae22481f 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb @@ -12,8 +12,4 @@ checksums = ['b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7'] license_server = 'license.example.com' -postinstallcmds = ['ln -s %(installdir)s/Executables/wolframscript %(installdir)s/bin/'] - -sanity_check_commands = ['mathematica --version'] - moduleclass = 'math' From bec0caf542eef5943bc7eb158fc11edddb222e59 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 May 2020 20:17:15 +0200 Subject: [PATCH 374/431] fix moduleclass for Ray, should be 'tools' --- .../easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb index d2f1e472dfd..e94dcd8d1cc 100644 --- a/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray/Ray-0.8.4-foss-2019b-Python-3.7.4.eb @@ -113,4 +113,4 @@ sanity_check_commands = [ 'ray --help' ] -moduleclass = 'bio' +moduleclass = 'tools' From 48882a3cb69ce429d175ebe86b4677e749cb55a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 May 2020 20:20:04 +0200 Subject: [PATCH 375/431] adding easyconfigs: DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb --- .../DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..0b457648a35 --- /dev/null +++ b/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-foss-2020a-R-4.0.0.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'DoubletFinder' +local_commit = '20654b8' +# see DESCRIPTION to determine version +version = '2.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/chris-mcginnis-ucsf/DoubletFinder' +description = "R package for detecting doublets in single-cell RNA sequencing data" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['fe0889618b11eb823f5c2232c6fe6fb989a917673590d0a3532642f31b74f36a'] + +dependencies = [ + ('R', '4.0.0'), + ('R-bundle-Bioconductor', '3.11', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From b839ad38d890b2776ddaab8a8b40a1151b3e17f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 May 2020 20:21:08 +0200 Subject: [PATCH 376/431] adding easyconfigs: harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb --- ...rmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..f9a8af0de99 --- /dev/null +++ b/easybuild/easyconfigs/h/harmony/harmony-1.0.0-20200224-foss-2020a-R-4.0.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'harmony' +local_commit = '88b1e2a' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0.0-20200224' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://portals.broadinstitute.org/harmony' +description = "Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets." + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/immunogenomics/harmony/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8e017d1525b0124ecda1f54fcbf74930d72f20b11b75f5e24443f4e200ee1eab'] + +dependencies = [ + ('R', '4.0.0'), + ('R-bundle-Bioconductor', '3.11', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' From 3f7a0e81302a101700a6e5e10173917fc4917e26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 May 2020 21:24:22 +0200 Subject: [PATCH 377/431] adding easyconfigs: MEM-20191023-foss-2020a-R-4.0.0.eb --- .../m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..78a75cf2a28 --- /dev/null +++ b/easybuild/easyconfigs/m/MEM/MEM-20191023-foss-2020a-R-4.0.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'MEM' +local_commit = '6b92476' +version = '20191023' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cytolab/mem' +description = "Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores." + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/cytolab/mem/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['735cc340fb644ddc4bd760d6897d3911561ea4735db10e799ff34e36ba138a86'] + +dependencies = [ + ('R', '4.0.0'), + ('R-bundle-Bioconductor', '3.11', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'tools' From ea8c6fe0af386750acd6bcb192213295743eb68b Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Sat, 9 May 2020 04:26:35 +0200 Subject: [PATCH 378/431] Add alternate checksum for EMBOSS --- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb index 4e1feaea3a3..e34109b6a96 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb @@ -29,7 +29,11 @@ source_urls = [GITHUB_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] checksums = [ - '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + ( + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', + '85f53a19125735e4a49fc25620d507fd86bf189e49096578924fe04893f2f7a9', + ), + # EMBOSS-6.6.0.tar.gz '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch ] From aa71af0ca6e07bf7e71f4473149c761bf9a7e17f Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 9 May 2020 08:50:32 +0000 Subject: [PATCH 379/431] Fix building rstudio on .deb systems --- .../r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb index 0f047779aa8..01aa0a3f504 100644 --- a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5033-fosscuda-2019b-Java-11.eb @@ -38,7 +38,9 @@ dependencies = [ ('Java', '11', '', True), ] -osdependencies = ['pam-devel'] +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] build_type = "Release" local_dep_dir = "%(builddir)s/%(name)s-%(version)s/dependencies/common" From aca843020ad5f5adf99923b1e496b5ce9292d438 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 10 May 2020 14:15:42 +0000 Subject: [PATCH 380/431] adding easyconfigs: csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb --- ...csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..148a9dfa9c5 --- /dev/null +++ b/easybuild/easyconfigs/c/csvkit/csvkit-1.0.5-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'csvkit' +version = '1.0.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/wireservice/csvkit' +description = """csvkit is a suite of command-line tools for converting to and working with CSV, + the king of tabular file formats.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [ + ('binutils', '2.32') +] + +dependencies = [ + ('Python', '3.7.4'), + ('openpyxl', '3.0.3', '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/*'] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('pytimeparse', '1.1.8', { + 'checksums': ['e86136477be924d7e670646a98561957e8ca7308d44841e21f5ddea757556a0a'], + }), + ('parsedatetime', '2.5', { + 'checksums': ['d2e9ddb1e463de871d32088a3f3cea3dc8282b1b2800e081bd0ef86900451667'], + }), + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '4.0.0', { + 'modulename': 'slugify', + 'checksums': ['a8fc3433821140e8f409a9831d13ae5deccd0b033d4744d94b31fea141bdd84c'], + }), + ('leather', '0.3.3', { + 'checksums': ['076d1603b5281488285718ce1a5ce78cf1027fe1e76adf9c548caf83c519b988'], + }), + ('agate', '1.6.1', { + 'checksums': ['c93aaa500b439d71e4a5cf088d0006d2ce2c76f1950960c8843114e5f361dfd3'], + }), + ('agate-excel', '0.2.3', { + 'modulename': 'agateexcel', + 'checksums': ['8f255ef2c87c436b7132049e1dd86c8e08bf82d8c773aea86f3069b461a17d52'], + }), + ('dbfread', '2.0.7', { + 'checksums': ['07c8a9af06ffad3f6f03e8fe91ad7d2733e31a26d2b72c4dd4cfbae07ee3b73d'], + }), + ('agate-dbf', '0.2.1', { + 'modulename': 'agatedbf', + 'checksums': ['00c93c498ec9a04cc587bf63dd7340e67e2541f0df4c9a7259d7cb3dd4ce372f'], + }), + ('SQLAlchemy', '1.3.16', { + 'checksums': ['7224e126c00b8178dfd227bc337ba5e754b197a3867d33b9f30dc0208f773d70'], + }), + ('agate-sql', '0.5.4', { + 'modulename': 'agatesql', + 'checksums': ['9277490ba8b8e7c747a9ae3671f52fe486784b48d4a14e78ca197fb0e36f281b'], + }), + (name, version, { + 'checksums': ['7bd390f4d300e45dc9ed67a32af762a916bae7d9a85087a10fd4f64ce65fd5b9'], + }), +] + +local_binaries = ['in2csv', 'sql2csv', 'csvclean', 'csvcut', 'csvgrep', 'csvjoin', 'csvsort', 'csvstack', 'csvformat', + 'csvjson', 'csvlook', 'csvpy', 'csvsql', 'csvstat'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [('csvlook', '-h')] + +moduleclass = 'tools' From 0368af212e3a63c010155ceb829d8d4ddf251c43 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Mon, 11 May 2020 12:32:35 +0200 Subject: [PATCH 381/431] Fix missing const qualifiers for ncurses (#10606) * Fix missing const qualifiers for ncurses * HTTPS link * Attribute ncurses patch with description * Attribute ncurses patch with description --- .../easyconfigs/n/ncurses/ncurses-5.9.eb | 8 ++- .../ncurses-5.9_fix-missing-const.patch | 52 +++++++++++++++++++ 2 files changed, 58 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-5.9_fix-missing-const.patch diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 38e9f531208..71d76d1c6a4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'ncurses' version = '5.9' -homepage = 'http://www.gnu.org/software/ncurses/' +homepage = 'https://www.gnu.org/software/ncurses/' description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" @@ -13,10 +13,14 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['ncurses-%(version)s_configure_darwin.patch'] +patches = [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', +] checksums = [ '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', # ncurses-5.9.tar.gz '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', # ncurses-5.9_configure_darwin.patch + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', # ncurses-5.9_fix-missing-const.patch ] # need to use -P preprocessor option for recent GCC versions (cfr. https://gcc.gnu.org/gcc-5/porting_to.html) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_fix-missing-const.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_fix-missing-const.patch new file mode 100644 index 00000000000..0ce462feb40 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_fix-missing-const.patch @@ -0,0 +1,52 @@ +Const-qualify member functions for newer compilers + +Ensure that some member functions are callable on const-qualified +objects with newer system compilers, as they will otherwise refuse to +compile the source. + +Author: Lars Viklund +diff -ru ncurses-5.9.orig/c++/cursesf.h ncurses-5.9/c++/cursesf.h +--- ncurses-5.9.orig/c++/cursesf.h 2005-08-13 20:08:24.000000000 +0200 ++++ ncurses-5.9/c++/cursesf.h 2020-04-02 16:03:10.219252152 +0200 +@@ -381,7 +381,7 @@ + uptr->m_user = user; + } + +- inline void *get_user() { ++ inline void *get_user() const { + UserHook* uptr = reinterpret_cast(::form_userptr (form)); + assert (uptr != 0 && uptr->m_back==this && uptr->m_owner==form); + return uptr->m_user; +diff -ru ncurses-5.9.orig/c++/cursesm.h ncurses-5.9/c++/cursesm.h +--- ncurses-5.9.orig/c++/cursesm.h 2005-08-13 20:10:36.000000000 +0200 ++++ ncurses-5.9/c++/cursesm.h 2020-04-02 16:03:21.407103674 +0200 +@@ -242,7 +242,7 @@ + uptr->m_user = user; + } + +- inline void *get_user() { ++ inline void *get_user() const { + UserHook* uptr = STATIC_CAST(UserHook*)(::menu_userptr (menu)); + assert (uptr != 0 && uptr->m_back==this && uptr->m_owner==menu); + return uptr->m_user; +diff -ru ncurses-5.9.orig/c++/cursesp.h ncurses-5.9/c++/cursesp.h +--- ncurses-5.9.orig/c++/cursesp.h 2008-08-16 19:20:23.000000000 +0200 ++++ ncurses-5.9/c++/cursesp.h 2020-04-02 16:03:29.522995966 +0200 +@@ -58,7 +58,7 @@ + const PANEL* m_owner; // the panel itself + } UserHook; + +- inline UserHook *UserPointer() ++ inline UserHook *UserPointer() const + { + UserHook* uptr = reinterpret_cast( + const_cast(::panel_userptr (p))); +@@ -77,7 +77,7 @@ + } + // Set the user pointer of the panel. + +- void *get_user() ++ void *get_user() const + { + UserHook* uptr = UserPointer(); + void *result = 0; From 03a48557441435d837ceb574180ab9c7c84c2212 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Mon, 11 May 2020 16:16:06 +0200 Subject: [PATCH 382/431] Fix Rmath paths --- easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-foss-2018b.eb b/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-foss-2018b.eb index 255a79c5028..fe5d926ec05 100644 --- a/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-foss-2018b.eb +++ b/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-foss-2018b.eb @@ -29,7 +29,7 @@ dependencies = [ ('Boost', '1.67.0'), ] -buildopts = 'INCMATH=$EBROOTLIBRMATH/include LIB_MATH=$EBROOTLIBRMATH/lib64/libRmath.a ' +buildopts = 'INC_MATH= LIB_MATH=-l:libRmath.a ' # we override LIB_BASE to change -lblas to $LIBBLAS (-lopenblas for foss toolchain) buildopts += 'LIB_BASE="-L$EBROOTBOOST/lib -lm -lz -lboost_iostreams -lboost_program_options -lgsl $LIBBLAS"' From 9d0832d0928b5207e662ab892a3dbe78ce0b6fce Mon Sep 17 00:00:00 2001 From: software Date: Mon, 11 May 2020 16:06:58 +0000 Subject: [PATCH 383/431] Update ALL, pRolocdata and geneLenDataBase extensions in Bioconductor/3.11 --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 024bac5a9a2..4112eae1147 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -301,8 +301,8 @@ exts_list = [ ('AgiMicroRna', '2.38.0', { 'checksums': ['d949f956deb889df596e28154d5f9200cc8d96ce97397fdb5ff3f5ec01c5ac6d'], }), - ('geneLenDataBase', '1.23.0', { - 'checksums': ['5b0bc46fa180d3a49abdc98eef89d26540d5f8597f4ed9ab37373af29f437cce'], + ('geneLenDataBase', '1.24.0', { + 'checksums': ['138408602210ca3c60b247842c0ff0c99e077cb71e07b3e1802b73cc4d2fa8a5'], }), ('goseq', '1.40.0', { 'checksums': ['d5d32fddd1a095ea264ccdd652e7e8988d06c624b94b6e2eb2fa43963389d9c7'], @@ -583,8 +583,8 @@ exts_list = [ ('pRoloc', '1.28.0', { 'checksums': ['64cf300eb4f869986756e2fd6c3adb9e28e8ceb5c10b9745b4bbf3d15989523c'], }), - ('pRolocdata', '1.25.3', { - 'checksums': ['24c9338d2ee56e33dce76f1e5ec82546468e983105be3c45beb68e732624e656'], + ('pRolocdata', '1.26.0', { + 'checksums': ['ff68cdd66f24521a7260c1483dee243b22c3baa6f685de7f8b1213b9442c879b'], }), ('pRolocGUI', '1.22.0', { 'checksums': ['0a88a6f3eef7512fe52ecd8ce0c759d8be73422f2f7257d381847334a7fb42b0'], @@ -703,8 +703,8 @@ exts_list = [ ('Seurat', '3.1.5', { 'checksums': ['757ef0e7697734aac5769705bef80dc7b95f006cdf52ae7034309a05f11578d1'], }), - ('ALL', '1.29.0', { - 'checksums': ['6e8d543de21ee98c00f487902077c55e8e8509bc3f09563dd09549807bfff6d8'], + ('ALL', '1.30.0', { + 'checksums': ['1fa870db73c1c113c1613518d0829f74ea90390030f8f3d92a87e8689ec820bf'], }), ('ConsensusClusterPlus', '1.52.0', { 'checksums': ['98fddf86255dc641beb3ccd8fd9b1c8ace430146ea87be3e0c750258921af819'], From 27ac33d4a2217ac605fe40ae52757480421ad8f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 May 2020 19:58:37 +0200 Subject: [PATCH 384/431] adding easyconfigs: GCC-10.1.0.eb --- .../b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb | 28 ++++++++++ .../binutils/binutils-2.34-GCCcore-10.1.0.eb | 40 +++++++++++++++ .../f/flex/flex-2.6.4-GCCcore-10.1.0.eb | 34 +++++++++++++ easybuild/easyconfigs/g/GCC/GCC-10.1.0.eb | 22 ++++++++ .../easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 51 +++++++++++++++++++ .../help2man-1.47.15-GCCcore-10.1.0.eb | 25 +++++++++ .../m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 33 ++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb | 26 ++++++++++ 8 files changed, 259 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-10.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb new file mode 100644 index 00000000000..b30667a9417 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.6.1' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1120f8bfe2cc13e5e1e3f671dc41b1a535ca5a75a70d5b349c19da9d4389f74d'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.34', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb new file mode 100644 index 00000000000..fb99acd8de8 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb @@ -0,0 +1,40 @@ +name = 'binutils' +version = '2.34' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '10.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = [ + 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', + 'binutils-%(version)s-readd-avx512-vmovd.patch', +] +checksums = [ + '53537d334820be13eeb8acb326d01c7c81418772d626715c7ae927a7d401cab3', # binutils-2.34.tar.gz + # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch + '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', + '45ecf7f5d198dd446d1a2e2a4d46b2747eb6fb8f2bfa18d7d42769e710e85716', # binutils-2.34-readd-avx512-vmovd.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.6.1'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.11'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb new file mode 100644 index 00000000000..e615af45793 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.6.1'), + ('help2man', '1.47.15'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.34', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-10.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-10.1.0.eb new file mode 100644 index 00000000000..797dfd61444 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-10.1.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '10.1.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.34', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb new file mode 100644 index 00000000000..bc096d39ad9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -0,0 +1,51 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '10.1.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.0.tar.bz2', + 'mpfr-4.0.2.tar.bz2', + 'mpc-1.1.0.tar.gz', + 'isl-0.22.1.tar.bz2', +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900', # gcc-10.1.0.tar.gz + 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 + 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 + '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz + '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.34'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb new file mode 100644 index 00000000000..2d8893f9c12 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.15' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '10.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['c25a35b30eceb315361484b0ff1f81c924e8ee5c8881576f1ee762f001dbcd1c'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.34', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb new file mode 100644 index 00000000000..9bd978b3ec9 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '10.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['M4-1.4.18_glibc_2.28.patch'] +checksums = [ + 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz + 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.34', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb new file mode 100644 index 00000000000..a7164e8d8fc --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '10.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.34', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From a63f448bd13b6993d47ac36942e5ebae01837ddc Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 12 May 2020 00:14:09 +0000 Subject: [PATCH 385/431] adding easyconfigs: libfabric-1.10.1-GCCcore-9.3.0.eb --- .../libfabric-1.10.1-GCCcore-9.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..822b4e3fed6 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.10.1-GCCcore-9.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.10.1' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['889fa8c99eed1ff2a5fd6faf6d5222f2cf38476b24f3b764f2cbb5900fee8284'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' From 7272a2fa1f72ff549660dcf290178c885659df31 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 12 May 2020 10:52:27 +1000 Subject: [PATCH 386/431] Create Stacks-2.53-foss-2019b.eb Upgrade to 2.53 Upgrade to foss-2019b Add https --- .../s/Stacks/Stacks-2.53-foss-2019b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb new file mode 100644 index 00000000000..47a7c64dc74 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.53' + +homepage = 'http://catchenlab.life.illinois.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee1efceaeeeb7a39f0c2e804ad7c0a003094db28c9101120c38ddb02846e90fd'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From ce8f21175ce47c9c1446bc90af49c3b72f31115d Mon Sep 17 00:00:00 2001 From: software Date: Tue, 12 May 2020 09:12:00 +0000 Subject: [PATCH 387/431] adding easyconfigs: rstudio-1.2.5042-foss-2019b-Java-11.eb --- .../rstudio-1.2.5042-foss-2019b-Java-11.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/r/rstudio/rstudio-1.2.5042-foss-2019b-Java-11.eb diff --git a/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5042-foss-2019b-Java-11.eb b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5042-foss-2019b-Java-11.eb new file mode 100644 index 00000000000..4e23ac822fd --- /dev/null +++ b/easybuild/easyconfigs/r/rstudio/rstudio-1.2.5042-foss-2019b-Java-11.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'rstudio' +version = '1.2.5042' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.rstudio.com/' +description = """This RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) +""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'rstudio-1.2.5033_fix_boost_170_compat.patch', + 'rstudio-1.2.5033_update_gwt.patch', +] +checksums = [ + '2bcd1d525d92e9ce42f4c7a57383c025e10d34313f8ed245429f02980b47c1fc', # v1.2.5042.tar.gz + 'd252111e28a7de8602b4df1f66b36dded260061f094b504895e5c789f8681091', # rstudio-1.2.5033_fix_boost_170_compat.patch + 'e0b4e165e45357bfaaefbd6f20a7ee69701c56bd623fa2bdfe6df4a1cabc4415', # rstudio-1.2.5033_update_gwt.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('CMake', '3.15.3'), + ('ant', '1.10.7', '-Java-%(javaver)s', True), +] + +dependencies = [ + ('Boost', '1.71.0'), + ('R', '3.6.2'), + ('Java', '11', '', True), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +build_type = "Release" +local_dep_dir = "%(builddir)s/%(name)s-%(version)s/dependencies/common" +preconfigopts = ("(cd %s && ./install-dictionaries && " + "./install-pandoc && ./install-mathjax && ./install-gwt) && ") % local_dep_dir +configopts = "-DRSTUDIO_TARGET=Server -DRSTUDIO_BOOST_SIGNALS_VERSION=2" + +sanity_check_paths = { + 'files': ["bin/rstudio-server"], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' From 7ef4cbb5c5a068eb1816b04829f8e76fc572817f Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Tue, 12 May 2020 13:59:29 +0200 Subject: [PATCH 388/431] add pytorch-1.4.0 suffix --- ...0-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb | 28 +++++++++++++++++++ ...sscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb create mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb new file mode 100644 index 00000000000..cfc96c497ed --- /dev/null +++ b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'torchaudio' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s-PyTorch-1.4.0' + +homepage = 'https://github.com/pytorch/audio' +description = """ Data manipulation and transformation for audio signal +processing, powered by PyTorch """ + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/audio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca27317dddcbe69c6586b03885534b3b50d666580843a5d22f1d605d47551807'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', '-Python-%(pyver)s'), + ('PyTorch', '1.4.0', '-Python-%(pyver)s'), + ('SoX', '14.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb new file mode 100644 index 00000000000..a982e8f38f9 --- /dev/null +++ b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'torchaudio' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s-PyTorch-1.4.0' + +homepage = 'https://github.com/pytorch/audio' +description = """ Data manipulation and transformation for audio signal +processing, powered by PyTorch """ + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/audio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca27317dddcbe69c6586b03885534b3b50d666580843a5d22f1d605d47551807'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', '-Python-%(pyver)s'), + ('PyTorch', '1.4.0', '-Python-%(pyver)s'), + ('SoX', '14.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 44885d60186576dd809bb3c44465247caf449cda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2020 14:09:34 +0200 Subject: [PATCH 389/431] add symlink for Arlequin commands + fix sanity check commands --- .../a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb index 88ef6fff349..f3614d0c5ab 100644 --- a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb +++ b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb @@ -48,9 +48,10 @@ components = [ }), ] -local_arlecore_bin = 'arlecore_linux/arlecore3522_64bit' +local_ver = ''.join(version.split('.')) +local_arlecore_bin = 'arlecore_linux/arlecore%s_64bit' % local_ver local_arlecore_sh = 'arlecore_linux/LaunchArlecore.sh' -local_arlsumstat_bin = 'arlsumstat_linux/arlsumstat3522_64bit' +local_arlsumstat_bin = 'arlsumstat_linux/arlsumstat%s_64bit' % local_ver, local_arlsumstat_sh = 'arlsumstat_linux/LaunchArlSumStat.sh' postinstallcmds = [ @@ -59,11 +60,13 @@ postinstallcmds = [ % (local_arlecore_bin, local_arlecore_sh), 'chmod +x %%(installdir)s/%s' % local_arlecore_bin, 'chmod +x %%(installdir)s/%s' % local_arlecore_sh, + 'cd %(installdir)s/arlecore_linux && ln -s arlecore3522_64bit arlecore', # fix arlsumstat 'sed -i "s@^arlsumstat=.*@arlsumstat=%%(installdir)s/%s@g" %%(installdir)s/%s' % (local_arlsumstat_bin, local_arlsumstat_sh), 'chmod +x %%(installdir)s/%s' % local_arlsumstat_bin, 'chmod +x %%(installdir)s/%s' % local_arlsumstat_sh, + 'cd %(installdir)s/arlsumstat_linux && ln -s arlsumstat3522_64bit arlsumstat', ] dependencies = [ ('R', '3.6.2'), @@ -72,12 +75,12 @@ dependencies = [ modextrapaths = {'PATH': ['arlecore_linux', 'arlsumstat_linux']} sanity_check_paths = { - 'files': [local_arlecore_bin, local_arlecore_sh, local_arlsumstat_bin, local_arlsumstat_sh], + 'files': ['arlecore_linux/arlecore', 'arlsumstat_linux/arlsumstat'], 'dirs': [], } sanity_check_commands = [ - 'LaunchArlecore.sh', - 'LaunchArlSumStat.sh', + "arlecore --help", + "arlsumstat --help", r'cd %(installdir)s/Example\ files_linux/ELB/ && LaunchArlecore.sh -s "Xdata.ars"', ] From f5b0f018cd6e261202a4f9bdd2aedbc687360fd7 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Tue, 12 May 2020 14:15:02 +0200 Subject: [PATCH 390/431] [foss/2020a] add extensions to R-4.0.0 and R-Bioconductor-3.11 --- ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 17 +++++++++++++++- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 20 ++++++++++++++++++- 2 files changed, 35 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 024bac5a9a2..f52e545d508 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -40,7 +40,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on May 7th 2020 +# packages updated on May 11th 2020 exts_list = [ ('readr', '1.3.1', { 'checksums': ['33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3'], @@ -766,6 +766,21 @@ exts_list = [ ('muscat', '1.2.0', { 'checksums': ['83c4a88e1cd87fcbe5395655fe02a07f9d00f211a46d547b11543d993436e1f7'], }), + ('IlluminaHumanMethylation450kmanifest', '0.4.0', { + 'checksums': ['41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763'], + }), + ('IlluminaHumanMethylationEPICmanifest', '0.3.0', { + 'checksums': ['e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a'], + }), + ('IlluminaHumanMethylation450kanno.ilmn12.hg19', '0.6.0', { + 'checksums': ['249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15'], + }), + ('IlluminaHumanMethylationEPICanno.ilm10b2.hg19', '0.6.0', { + 'checksums': ['4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69'], + }), + ('conumee', '1.22.0', { + 'checksums': ['cdbbf1ee7e87422b21e2d938559c1b30ce81cc4ccf0bbd9f06a74f5cb162f972'], + }), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 830132ae874..4bbf74ee10e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -70,7 +70,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 29 April 2020 +# packages updated on 11 May 2020 exts_list = [ 'base', 'datasets', @@ -2406,6 +2406,24 @@ exts_list = [ ('ggnetwork', '0.5.8', { 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], }), + ('rstantools', '2.0.0', { + 'checksums': ['4ae78aa39c3d4897f453e621a09961d6f2cda27a1b5657d4d4b32d3d89bd80c6'], + }), + ('bayesplot', '1.7.1', { + 'checksums': ['820ca9ca3258fc68333e75fd60898c0d0f08f513b66c161ca6159a54ad54006b'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.16', { + 'checksums': ['3f728c6a5153dca28f69b9355ae9d18c5f7e70d12495c0c047eef673c1053116'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('brms', '2.12.0', { + 'checksums': ['fa21505dca65d027f1cf1c573258de5f3c51ca8b94abd6dcf9123a3a27a72999'], + }), ] moduleclass = 'lang' From 4950410cb50427734c3b25b76d6d13683e2437d1 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Tue, 12 May 2020 14:49:23 +0200 Subject: [PATCH 391/431] remove easyconfigs with wrong suffix --- ...orchaudio-0.5.0-foss-2019b-Python-3.7.4.eb | 28 ------------------- ...audio-0.5.0-fosscuda-2019b-Python-3.7.4.eb | 28 ------------------- 2 files changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb delete mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb deleted file mode 100644 index 044fc75d85a..00000000000 --- a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-foss-2019b-Python-3.7.4.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'torchaudio' -version = '0.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pytorch/audio' -description = """ Data manipulation and transformation for audio signal -processing, powered by PyTorch """ - -toolchain = {'name': 'foss', 'version': '2019b'} - -source_urls = ['https://github.com/pytorch/audio/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['ca27317dddcbe69c6586b03885534b3b50d666580843a5d22f1d605d47551807'] - -dependencies = [ - ('Python', '3.7.4'), - ('SciPy-bundle', '2019.10', versionsuffix), - ('PyTorch', '1.4.0', versionsuffix), - ('SoX', '14.4.2'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb deleted file mode 100644 index d003fc3a66f..00000000000 --- a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.5.0-fosscuda-2019b-Python-3.7.4.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'torchaudio' -version = '0.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pytorch/audio' -description = """ Data manipulation and transformation for audio signal -processing, powered by PyTorch """ - -toolchain = {'name': 'fosscuda', 'version': '2019b'} - -source_urls = ['https://github.com/pytorch/audio/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['ca27317dddcbe69c6586b03885534b3b50d666580843a5d22f1d605d47551807'] - -dependencies = [ - ('Python', '3.7.4'), - ('SciPy-bundle', '2019.10', versionsuffix), - ('PyTorch', '1.4.0', versionsuffix), - ('SoX', '14.4.2'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'tools' From a2a1598a2aeb18c60f0fa85f660ccefc21e43387 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 12 May 2020 17:10:33 +0200 Subject: [PATCH 392/431] add 2 extensions for Perl-5.30.2 --- .../easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index 8b6edb3963a..782961d6d4f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -7,7 +7,7 @@ description = """Larry Wall's Practical Extraction and Report Language""" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] checksums = ['66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'] @@ -1722,6 +1722,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/'], 'checksums': ['087ad6d6a495d823771e5bc23bcbcd31c683289b5cb45fc4e857449f9ea7aa1b'], }), + ('Text::CSV_XS', '1.41', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND/'], + 'checksums': ['0e4b7be423c02f09135a75082cb00136ff6a69cff25b012089048ea030f173ab'], + }), + ('DBD::CSV', '0.54', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND/'], + 'checksums': ['bc597cd7195e5a023e2b3413d8dc614602b9b3f279f436027881796464d4f0be'], + }), ] moduleclass = 'lang' From 8cb6d85655614e867caaac4a93f5e7ad620c6fb5 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 12 May 2020 19:52:51 +0200 Subject: [PATCH 393/431] adding easyconfigs: angsd-0.933-GCC-8.3.0.eb, angsd-0.933-iccifort-2019.5.281.eb --- .../a/angsd/angsd-0.933-GCC-8.3.0.eb | 36 +++++++++++++++++++ .../angsd/angsd-0.933-iccifort-2019.5.281.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.933-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.933-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.933-GCC-8.3.0.eb b/easybuild/easyconfigs/a/angsd/angsd-0.933-GCC-8.3.0.eb new file mode 100644 index 00000000000..0a5c05778cb --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.933-GCC-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.933' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/ANGSD/angsd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2f992325dc08fa25ac525d9300ef6bd61808e74c521b4cc72a2ce00d98f402bb'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.4'), + ('HTSlib', '1.10.2'), +] + +files_to_copy = [ + (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', + 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', + 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', + 'misc/ibs'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.933-iccifort-2019.5.281.eb b/easybuild/easyconfigs/a/angsd/angsd-0.933-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..e1f06d9fd59 --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.933-iccifort-2019.5.281.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.933' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://github.com/ANGSD/angsd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2f992325dc08fa25ac525d9300ef6bd61808e74c521b4cc72a2ce00d98f402bb'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.4'), + ('HTSlib', '1.10.2'), +] + +files_to_copy = [ + (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', + 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', + 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', + 'misc/ibs'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + + +moduleclass = 'bio' From d20e84e84bab65525ee70d1de36efb9477d9c50e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2020 19:50:42 +0200 Subject: [PATCH 394/431] add patch for h5py 2.10.0 with 2020a toolchains to avoid MPI_Init at import --- .../h5py-2.10.0-foss-2020a-Python-3.8.2.eb | 10 +++--- .../h5py-2.10.0-intel-2020a-Python-3.8.2.eb | 10 +++--- .../h/h5py/h5py-2.10.0_fix-import-mpi.patch | 35 +++++++++++++++++++ 3 files changed, 45 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb index 010d200891a..962f7ffe264 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb @@ -14,7 +14,11 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] +patches = ['h5py-%(version)s_fix-import-mpi.patch'] +checksums = [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + 'eb14f2983e84a05a5e04c42c0bf00d9d1d128fb0bed105d0b6bf574f82e246cd', # h5py-2.10.0_fix-import-mpi.patch +] builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] @@ -30,8 +34,4 @@ download_dep_fail = True # to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' -# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) -options = {'modulename': False} -sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb index 71353b9b531..3f9c928fc4f 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb @@ -14,7 +14,11 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] +patches = ['h5py-%(version)s_fix-import-mpi.patch'] +checksums = [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + 'eb14f2983e84a05a5e04c42c0bf00d9d1d128fb0bed105d0b6bf574f82e246cd', # h5py-2.10.0_fix-import-mpi.patch +] builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] @@ -30,8 +34,4 @@ download_dep_fail = True # to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' -# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) -options = {'modulename': False} -sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch b/easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch new file mode 100644 index 00000000000..14b4abbc6c5 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch @@ -0,0 +1,35 @@ +avoid that mpi4py initializes MPI at import, +only initialize when needed +cfr. https://github.com/h5py/h5py/pull/1544 +author: Kenneth Hoste (HPC-UGent) +diff -ru h5py-2.10.0.orig/h5py/_hl/files.py h5py-2.10.0/h5py/_hl/files.py +--- h5py-2.10.0.orig/h5py/_hl/files.py 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/_hl/files.py 2020-05-12 17:56:43.503885936 +0200 +@@ -44,6 +44,8 @@ + + def _set_fapl_mpio(plist, **kwargs): + import mpi4py ++ if not mpi4py.MPI.Is_initialized(): ++ mpi4py.MPI.Init() + kwargs.setdefault('info', mpi4py.MPI.Info()) + plist.set_fapl_mpio(**kwargs) + +diff -ru h5py-2.10.0.orig/h5py/__init__.py h5py-2.10.0/h5py/__init__.py +--- h5py-2.10.0.orig/h5py/__init__.py 2019-09-06 23:33:01.000000000 +0200 ++++ h5py-2.10.0/h5py/__init__.py 2020-05-12 17:56:12.603359778 +0200 +@@ -16,6 +16,15 @@ + + from warnings import warn as _warn + ++# Tell mpi4py to not automatically initialize MPI at import; ++# required to avoid problems with 'import h5py' in some environment ++# when h5py was built with MPI support ++try: ++ import mpi4py ++ mpi4py.rc.initialize = False ++ mpi4py.rc.finalize = True ++except ImportError: ++ pass + + # --- Library setup ----------------------------------------------------------- + From 8cc8c053638b04fc2cdbad0dd758ff9ef20cff73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2020 20:02:40 +0200 Subject: [PATCH 395/431] drop mpirun workaround in yaff easyconfig using intel/2020a toolchain (no longer needed after fix for h5py in d20e84e84b) --- .../y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb | 5 ----- .../y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 11 ----------- 2 files changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb index a1215832a8a..c10d1b80601 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020a-Python-3.8.2.eb @@ -39,9 +39,4 @@ check_ldshared = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " runtest += "python setup.py build_ext -i; nosetests -v" -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb index 162894aaf51..071c10f709c 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb @@ -42,15 +42,4 @@ check_ldshared = True # runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " # runtest += "python setup.py build_ext -i; %(mpi_cmd_prefix)s nosetests -v" -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# skip regular 'import yaff', and run it via mpirun (since 'import yaff' results in an MPI_Init call via h5py) -# this is only needed because of a bug in Intel MPI 2019 update 7 ("Fatal error in PMPI_Init_thread") -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/10213 -options = {'modulename': False} -sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] - moduleclass = 'chem' From ab4156dfa4ff4e2558006768946cf7719c516bbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2020 20:26:33 +0200 Subject: [PATCH 396/431] fix Mako easyconfigs using a 2016 & 2017 toolchain (cfr. #10462) --- .../Mako-1.0.4-foss-2016b-Python-2.7.12.eb | 26 ++++++++++++++----- .../Mako-1.0.4-intel-2016b-Python-2.7.12.eb | 25 +++++++++++++----- .../Mako-1.0.6-foss-2017a-Python-2.7.13.eb | 25 ++++++++++++------ .../Mako-1.0.6-intel-2017a-Python-2.7.13.eb | 22 ++++++++++++---- .../Mako-1.0.7-foss-2017b-Python-2.7.14.eb | 23 +++++++++++----- ...Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb | 22 +++++++++++----- .../Mako-1.0.7-intel-2017b-Python-2.7.14.eb | 23 +++++++++++----- ...ako-1.0.7-intelcuda-2017b-Python-2.7.14.eb | 22 +++++++++++----- 8 files changed, 136 insertions(+), 52 deletions(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb index 057c889c190..aa1648fa036 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-foss-2016b-Python-2.7.12.eb @@ -1,23 +1,35 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['fed99dbe4d0ddb27a33ee4910d8708aca9ef1fe854e668387a9ab9a90cbf9059'] - dependencies = [('Python', '2.7.12')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['fed99dbe4d0ddb27a33ee4910d8708aca9ef1fe854e668387a9ab9a90cbf9059'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +# pip 8.1.2 (included with Python 2.7.12) doesn't support 'pip check' yet +sanity_pip_check = False + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb index 4817748dbce..92bfc1f2e0b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.4-intel-2016b-Python-2.7.12.eb @@ -1,22 +1,35 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [('Python', '2.7.12')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['fed99dbe4d0ddb27a33ee4910d8708aca9ef1fe854e668387a9ab9a90cbf9059'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +# pip 8.1.2 (included with Python 2.7.12) doesn't support 'pip check' yet +sanity_pip_check = False + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb index 0f724f7b475..4749ddd3c97 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.6' @@ -9,17 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'foss', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = [ - '48559ebd872a8e77f92005884b3d88ffae552812cdf17db6768e5c3be5ebbe0d', # Mako-1.0.6.tar.gz -] - dependencies = [('Python', '2.7.13')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['48559ebd872a8e77f92005884b3d88ffae552812cdf17db6768e5c3be5ebbe0d'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb index 9bae4651685..f758d7149f9 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.6' @@ -9,14 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] - dependencies = [('Python', '2.7.13')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['48559ebd872a8e77f92005884b3d88ffae552812cdf17db6768e5c3be5ebbe0d'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb index 38e5f06bc8b..086564fdca6 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb index 323b63bda50..401480cb428 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,18 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'fosscuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] use_pip = True -download_dep_fail = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg-info'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb index ba493f56eb5..600668e4a83 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,15 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] + sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb index 918a6d7e6bf..2e35f7b0fc7 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'Mako' version = '1.0.7' @@ -9,18 +9,26 @@ description = """A super-fast templating language that borrows the best ideas fr toolchain = {'name': 'intelcuda', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - dependencies = [('Python', '2.7.14')] use_pip = True -download_dep_fail = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + (name, version, { + 'checksums': ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'], + }), +] sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg-info'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } +sanity_pip_check = True + moduleclass = 'devel' From e89361723905d9540ae31ef63dea4c3d3b76a87e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2020 21:01:13 +0200 Subject: [PATCH 397/431] add Mako 1.0.4 easyconfigs using Python 2.7.12 to whitelist for not having sanity_pip_check enabled --- test/easyconfigs/easyconfigs.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5efed20d6a8..c5fea851575 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -552,6 +552,8 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): # These packages do not support installation with 'pip' whitelist_pip = [r'MATLAB-Engine-.*', r'PyTorch-.*', r'Meld-.*'] + whitelist_pip_check = [r'Mako-1.0.4.*Python-2.7.12.*'] + failing_checks = [] for ec in changed_ecs: @@ -609,7 +611,8 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): if use_pip and easyblock in ['PythonBundle', 'PythonPackage']: sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip): - failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn) + if not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): + failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn) self.assertFalse(failing_checks, '\n'.join(failing_checks)) From 8ae4692bac1c4717cb31f5ceee8910908e4b224d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 May 2020 21:25:19 +0200 Subject: [PATCH 398/431] use https in homepage for Mako --- .../easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb | 2 +- .../m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb | 2 +- .../m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb index 4749ddd3c97..998e83cb614 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-foss-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'foss', 'version': '2017a'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb index f758d7149f9..6d556cd86fa 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.6-intel-2017a-Python-2.7.13.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.6' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2017a'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb index 086564fdca6..16ec8b1aa98 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'foss', 'version': '2017b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb index 401480cb428..092a64f05b2 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'fosscuda', 'version': '2017b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb index 600668e4a83..2208f39b88d 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intel', 'version': '2017b'} diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb index 2e35f7b0fc7..2fd2e1001b0 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'Mako' version = '1.0.7' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.makotemplates.org' +homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" toolchain = {'name': 'intelcuda', 'version': '2017b'} From 5ccc17a22f852a2185e9cd3b9073cf6b85a2a1fd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 12 May 2020 23:35:54 +0200 Subject: [PATCH 399/431] adding easyconfigs: Julia-1.4.1-linux-x86_64.eb --- .../j/Julia/Julia-1.4.1-linux-x86_64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.4.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.4.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.4.1-linux-x86_64.eb new file mode 100644 index 00000000000..5fbfcfe22cc --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.4.1-linux-x86_64.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.4.1' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['fd6d8cadaed678174c3caefb92207a3b0e8da9f926af6703fb4d1e4e4f50610a'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lang' From 7bd61fc7edda94550422bc20360a3d428f09af2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 13 May 2020 00:43:26 +0200 Subject: [PATCH 400/431] Update easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb Co-authored-by: Sam Moors --- .../easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb index 0d2d255e29f..f1cea13d3a6 100644 --- a/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NLMpy/NLMpy-0.1.5-intel-2019b-Python-3.7.4.eb @@ -23,4 +23,4 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -moduleclass = 'bio' +moduleclass = 'geo' From 8bbac0ca53a3209416462ecca631041d3049553b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 13 May 2020 00:49:31 +0200 Subject: [PATCH 401/431] Update easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb Co-authored-by: Lars Viklund --- .../easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb index 686a59fa8c4..989ce387e07 100644 --- a/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HDDM/HDDM-0.7.5-intel-2019b-Python-3.7.4.eb @@ -5,7 +5,7 @@ version = '0.7.5' versionsuffix = '-Python-%(pyver)s' homepage = 'http://ski.clps.brown.edu/hddm_docs' -description = """HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation +description = """HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC).""" toolchain = {'name': 'intel', 'version': '2019b'} From 76a06c92046761505fe515e360a46e255debb6f7 Mon Sep 17 00:00:00 2001 From: zao Date: Wed, 13 May 2020 01:36:14 +0200 Subject: [PATCH 402/431] Fix binutils for Fedora 32 / GCC 10 --- .../easyconfigs/b/binutils/binutils-2.28.eb | 6 ++++- .../easyconfigs/b/binutils/binutils-2.30.eb | 6 ++++- .../easyconfigs/b/binutils/binutils-2.31.1.eb | 8 +++++- .../binutils/binutils-2.31.1_fix_gcc10.patch | 26 +++++++++++++++++++ .../easyconfigs/b/binutils/binutils-2.32.eb | 5 ++-- ...nutils-2.32_gold-include-cpp-headers.patch | 17 ++++++++++++ 6 files changed, 63 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.32_gold-include-cpp-headers.patch diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index 6cc53f407ef..d837daaceea 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -9,7 +9,11 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] +patches = ['binutils-2.32_gold-include-cpp-headers.patch'] +checksums = [ + 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz + 'b695652e0886af4eb0a2d220f4721c6c4d8b2d96fb3d62b213fee305a02bdf5b', # binutils-2.32_gold-include-cpp-headers.patch +] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb index 38a49858892..2397b30acf3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb @@ -9,10 +9,14 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['binutils-%(version)s_fix-assertion-fail-elf.patch'] +patches = [ + 'binutils-%(version)s_fix-assertion-fail-elf.patch', + 'binutils-2.32_gold-include-cpp-headers.patch', +] checksums = [ '8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea', # binutils-2.30.tar.gz '7a661190c973287642296dd9fb30ff45dc26ae2138f7761cd8362f7e412ff5ab', # binutils-2.30_fix-assertion-fail-elf.patch + 'b695652e0886af4eb0a2d220f4721c6c4d8b2d96fb3d62b213fee305a02bdf5b', # binutils-2.32_gold-include-cpp-headers.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb index 6f1e5fab26e..6de0335c1e6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb @@ -9,11 +9,17 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['binutils-2.31.1-gold-ignore-discarded-note-relocts.patch'] +patches = [ + 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', + 'binutils-2.32_gold-include-cpp-headers.patch', + 'binutils-2.31.1_fix_gcc10.patch', +] checksums = [ 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', + 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch + '75bc1c8fa1b5e9be9e54bdd79bd51a33669268d26ea14136c7d58cc6cc1e52f7', # binutils-2.31.1_fix_gcc10.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch b/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch new file mode 100644 index 00000000000..8721575710a --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch @@ -0,0 +1,26 @@ +Widen integer type compared to enum + +GCC 10 seems to enforce signedness between types when comparing values. + +Author: Lars Viklund +diff -ru binutils-2.31.1.orig/gold/x86_64.cc binutils-2.31.1/gold/x86_64.cc +--- binutils-2.31.1.orig/gold/x86_64.cc 2018-06-24 20:38:57.000000000 +0200 ++++ binutils-2.31.1/gold/x86_64.cc 2020-05-13 00:56:30.254725766 +0200 +@@ -1585,7 +1585,7 @@ + { + uint32_t val = 0; + +- switch (pr_type) ++ switch ((size_t)(uint32_t)pr_type) + { + case elfcpp::GNU_PROPERTY_X86_ISA_1_USED: + case elfcpp::GNU_PROPERTY_X86_ISA_1_NEEDED: +@@ -1606,7 +1606,7 @@ + break; + } + +- switch (pr_type) ++ switch ((size_t)(uint32_t)pr_type) + { + case elfcpp::GNU_PROPERTY_X86_ISA_1_USED: + this->isa_1_used_ |= val; diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb index 500c0fcc964..18be76fd5f7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb @@ -12,13 +12,14 @@ sources = [SOURCE_TAR_GZ] patches = [ 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', 'binutils-2.32-readd-avx512-vmovd.patch', + 'binutils-2.32_gold-include-cpp-headers.patch', ] checksums = [ '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', - # binutils-2.32-readd-avx512-vmovd.patch - '9e16ba3acd9af473a882e2d4c81ca024fdd62dc332eb527cc778fc9d31f01939', + '9e16ba3acd9af473a882e2d4c81ca024fdd62dc332eb527cc778fc9d31f01939', # binutils-2.32-readd-avx512-vmovd.patch + 'b695652e0886af4eb0a2d220f4721c6c4d8b2d96fb3d62b213fee305a02bdf5b', # binutils-2.32_gold-include-cpp-headers.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32_gold-include-cpp-headers.patch b/easybuild/easyconfigs/b/binutils/binutils-2.32_gold-include-cpp-headers.patch new file mode 100644 index 00000000000..724b77e6123 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32_gold-include-cpp-headers.patch @@ -0,0 +1,17 @@ +Ensure that std::string is present + +Compilers occasionally change what headers include which, in this case +GCC 10 got rid of from some include chain. + +Author: Lars Viklund +diff -ru binutils-2.32.orig/gold/errors.h binutils-2.32/gold/errors.h +--- binutils-2.32.orig/gold/errors.h 2019-01-19 17:01:33.000000000 +0100 ++++ binutils-2.32/gold/errors.h 2020-05-12 23:54:47.670016324 +0200 +@@ -24,6 +24,7 @@ + #define GOLD_ERRORS_H + + #include ++#include + + #include "gold-threads.h" + From ad0fdb2ba003e6916a37581aaad463a424879c69 Mon Sep 17 00:00:00 2001 From: zao Date: Wed, 13 May 2020 01:43:27 +0200 Subject: [PATCH 403/431] Update checksums, HTTPS URLs --- easybuild/easyconfigs/b/binutils/binutils-2.28.eb | 4 ++-- easybuild/easyconfigs/b/binutils/binutils-2.30.eb | 4 ++-- easybuild/easyconfigs/b/binutils/binutils-2.32.eb | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index d837daaceea..987fcb83ab2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -1,7 +1,7 @@ name = 'binutils' version = '2.28' -homepage = 'http://directory.fsf.org/project/binutils/' +homepage = 'https://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] patches = ['binutils-2.32_gold-include-cpp-headers.patch'] checksums = [ 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz - 'b695652e0886af4eb0a2d220f4721c6c4d8b2d96fb3d62b213fee305a02bdf5b', # binutils-2.32_gold-include-cpp-headers.patch + 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb index 2397b30acf3..bb473df1b22 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb @@ -1,7 +1,7 @@ name = 'binutils' version = '2.30' -homepage = 'http://directory.fsf.org/project/binutils/' +homepage = 'https://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" @@ -16,7 +16,7 @@ patches = [ checksums = [ '8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea', # binutils-2.30.tar.gz '7a661190c973287642296dd9fb30ff45dc26ae2138f7761cd8362f7e412ff5ab', # binutils-2.30_fix-assertion-fail-elf.patch - 'b695652e0886af4eb0a2d220f4721c6c4d8b2d96fb3d62b213fee305a02bdf5b', # binutils-2.32_gold-include-cpp-headers.patch + 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb index 18be76fd5f7..be3aabd8389 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb @@ -19,7 +19,7 @@ checksums = [ # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', '9e16ba3acd9af473a882e2d4c81ca024fdd62dc332eb527cc778fc9d31f01939', # binutils-2.32-readd-avx512-vmovd.patch - 'b695652e0886af4eb0a2d220f4721c6c4d8b2d96fb3d62b213fee305a02bdf5b', # binutils-2.32_gold-include-cpp-headers.patch + 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch ] builddependencies = [ From 1fd7fd6e9e42afc57279ca789deaa8bd13f9840b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 08:28:37 +0200 Subject: [PATCH 404/431] use https in source URLs for GffCompare MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb index cde06a619f9..a1a60272ae7 100644 --- a/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.11.6-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ description = """GffCompare provides classification and reference annotation map toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['6095d97301a9c8dbd5e99e8c42860ce5953546277a09a0b46c835019815f6174'] From 5b137587ab890af5c0b2957ef8de467757176171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 08:29:18 +0200 Subject: [PATCH 405/431] use https in homepage for MultiQC MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb index 06577a12e1d..e089f8aff21 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-3.7.4.eb @@ -14,7 +14,7 @@ name = 'MultiQC' version = '1.8' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. From acc7b0d50697e48ea12b20f670eb8954b78a5a0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 08:30:17 +0200 Subject: [PATCH 406/431] use https in homepage for MultiQC MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb index 7851c93c45d..a2347c8e202 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.8-intel-2019b-Python-2.7.16.eb @@ -14,7 +14,7 @@ name = 'MultiQC' version = '1.8' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://multiqc.info' +homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. From 2c2cd3c6b9a5a2a869de622023e79d5fed42347f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 08:30:53 +0200 Subject: [PATCH 407/431] avoid hardcoding version in RNA-Bloom easyconfig MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb index 930af7a4bdc..dbd242572b8 100644 --- a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb @@ -9,7 +9,7 @@ description = "RNA-Bloom is a fast and memory-efficient de novo transcript seque toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/v1.2.3'] -sources = ['rnabloom_v1.2.3.tar.gz'] +sources = ['rnabloom_v%(version)s.tar.gz'] checksums = ['7418761ff99f24f0edc23772cfa517c3d7401eac98642dcb017d48fb35c6ee4a'] dependencies = [ From 3fc01249f2159e3d25dc248a6a9ab7b0a8a067a0 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 13 May 2020 09:31:17 +0000 Subject: [PATCH 408/431] Removed the perl-suffix as requsted --- ....0-Python-3.7.4.eb => MEME-5.1.1-foss-2019b-Python-3.7.4.eb} | 2 +- ...0-Python-3.7.4.eb => MEME-5.1.1-intel-2019b-Python-3.7.4.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/MEME/{MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb => MEME-5.1.1-foss-2019b-Python-3.7.4.eb} (96%) rename easybuild/easyconfigs/m/MEME/{MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb => MEME-5.1.1-intel-2019b-Python-3.7.4.eb} (96%) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb similarity index 96% rename from easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb rename to easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb index 07ae04b54ba..ac176c5c489 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'MEME' version = '5.1.1' -versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://meme-suite.org' description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb similarity index 96% rename from easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb rename to easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb index 8eefbb8b55f..9ac8e36aadb 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Perl-5.30.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'MEME' version = '5.1.1' -versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://meme-suite.org' description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or From f17cc2b28713a2863ff7d7edecd0be4e22cd9372 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 11:30:55 +0200 Subject: [PATCH 409/431] don't use harmful patch for h5py 2.10.0 with foss/2020a + pull out h5py 2.10.0 easyconfig using intel/2020a --- .../h5py-2.10.0-foss-2020a-Python-3.8.2.eb | 6 +-- .../h5py-2.10.0-intel-2020a-Python-3.8.2.eb | 37 --------------- .../h/h5py/h5py-2.10.0_fix-import-mpi.patch | 35 --------------- .../yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 45 ------------------- 4 files changed, 1 insertion(+), 122 deletions(-) delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch delete mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb index 962f7ffe264..2965e1735c6 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020a-Python-3.8.2.eb @@ -14,11 +14,7 @@ toolchainopts = {'usempi': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_fix-import-mpi.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - 'eb14f2983e84a05a5e04c42c0bf00d9d1d128fb0bed105d0b6bf574f82e246cd', # h5py-2.10.0_fix-import-mpi.patch -] +checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 3f9c928fc4f..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_fix-import-mpi.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - 'eb14f2983e84a05a5e04c42c0bf00d9d1d128fb0bed105d0b6bf574f82e246cd', # h5py-2.10.0_fix-import-mpi.patch -] - -builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -use_pip = False -download_dep_fail = True - -# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip -prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch b/easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch deleted file mode 100644 index 14b4abbc6c5..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0_fix-import-mpi.patch +++ /dev/null @@ -1,35 +0,0 @@ -avoid that mpi4py initializes MPI at import, -only initialize when needed -cfr. https://github.com/h5py/h5py/pull/1544 -author: Kenneth Hoste (HPC-UGent) -diff -ru h5py-2.10.0.orig/h5py/_hl/files.py h5py-2.10.0/h5py/_hl/files.py ---- h5py-2.10.0.orig/h5py/_hl/files.py 2019-09-06 23:29:33.000000000 +0200 -+++ h5py-2.10.0/h5py/_hl/files.py 2020-05-12 17:56:43.503885936 +0200 -@@ -44,6 +44,8 @@ - - def _set_fapl_mpio(plist, **kwargs): - import mpi4py -+ if not mpi4py.MPI.Is_initialized(): -+ mpi4py.MPI.Init() - kwargs.setdefault('info', mpi4py.MPI.Info()) - plist.set_fapl_mpio(**kwargs) - -diff -ru h5py-2.10.0.orig/h5py/__init__.py h5py-2.10.0/h5py/__init__.py ---- h5py-2.10.0.orig/h5py/__init__.py 2019-09-06 23:33:01.000000000 +0200 -+++ h5py-2.10.0/h5py/__init__.py 2020-05-12 17:56:12.603359778 +0200 -@@ -16,6 +16,15 @@ - - from warnings import warn as _warn - -+# Tell mpi4py to not automatically initialize MPI at import; -+# required to avoid problems with 'import h5py' in some environment -+# when h5py was built with MPI support -+try: -+ import mpi4py -+ mpi4py.rc.initialize = False -+ mpi4py.rc.finalize = True -+except ImportError: -+ pass - - # --- Library setup ----------------------------------------------------------- - diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 071c10f709c..00000000000 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,45 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# -# Building this in interactive Slurm session will result in freeze during either -# runtest phase or sanity_check_commands phase (python -c 'import yaff') -# -# If you submit this as non-interactive Slurm job, it will build just fine. -# Possibly root cause: https://github.com/h5py/h5py/issues/917 -# -easyblock = 'PythonPackage' - -name = 'yaff' -version = '1.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/yaff/' -description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] - -dependencies = [ - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('molmod', '1.4.5', versionsuffix), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -# disable tests when installing with intel/2020a, due to bug in Intel MPI 2019 update 7; -# commands that trigger an MPI_Init crash with "Fatal error in PMPI_Init_thread" if they're not run via mpirun, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/10213 -# runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -# runtest += "python setup.py build_ext -i; %(mpi_cmd_prefix)s nosetests -v" - -moduleclass = 'chem' From d915c443b6aed9ff6acb042c4d3217478311f6d5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 13 May 2020 14:26:24 +0200 Subject: [PATCH 410/431] adding easyconfigs: parallel-20200422-GCCcore-9.3.0.eb --- .../parallel-20200422-GCCcore-9.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20200422-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20200422-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20200422-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e93c91645e5 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20200422-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20200422' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['4bdebf91cc39ea54dec384ad475463cb7c2758fda2ae4a30111e7cfdb3c85530'] + +builddependencies = [('binutils', '2.34')] +dependencies = [ + ('Perl', '5.30.2'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' From 99d18771369e33bcc804162840b8f14cf3c52b06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 15:05:30 +0200 Subject: [PATCH 411/431] remove h5py & yaff easyconfigs using intel/2020a until MPI_Init issues in h5py are resolved (cfr. #10630) --- .../h5py-2.10.0-intel-2020a-Python-3.8.2.eb | 37 --------------- .../yaff-1.6.0-intel-2020a-Python-3.8.2.eb | 47 ------------------- 2 files changed, 84 deletions(-) delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb delete mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 71353b9b531..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] - -builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('HDF5', '1.10.6'), -] - -use_pip = False -download_dep_fail = True - -# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip -prebuildopts = 'python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) -options = {'modulename': False} -sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index 4846a904a7c..00000000000 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,47 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# -# Building this in interactive session will result in freeze during either -# runtest phase or sanity_check_commands phase (python -c 'import yaff') -# -# If you submit this at non-interactive job, it will build just fine. -# Possibly root cause: https://github.com/h5py/h5py/issues/917 -# -easyblock = 'PythonPackage' - -name = 'yaff' -version = '1.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://molmod.github.io/yaff/' -description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] - -dependencies = [ - ('Python', '3.8.2'), - ('h5py', '2.10.0', versionsuffix), - ('molmod', '1.4.5', versionsuffix), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'chem' From 9edf80c3dafb217dec1d3d870581b618d0c7b4be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 18:38:05 +0200 Subject: [PATCH 412/431] stop using old hpcugent URL for cloning framework/easyblocks repos in CI (even though it auto-redirects) --- .github/workflows/unit_tests.yml | 2 +- .travis.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 12891fa4a77..f354aedc873 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -55,7 +55,7 @@ jobs: cd easybuild-framework; git log -n 1; cd - pip install $PWD/easybuild-framework - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-easyblocks.git + git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-easyblocks.git cd easybuild-easyblocks; git log -n 1; cd - pip install $PWD/easybuild-easyblocks diff --git a/.travis.yml b/.travis.yml index 182a6bd20b9..08882713ab7 100644 --- a/.travis.yml +++ b/.travis.yml @@ -27,10 +27,10 @@ install: - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; fi - if [ "x$TRAVIS_BRANCH" = 'x4.x' ]; then BRANCH=4.x; fi - cd $HOME - - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-framework.git - cd easybuild-framework; git log -n 1; cd - - pip install $PWD/easybuild-framework - - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-easyblocks.git + - git clone -b $BRANCH --depth 10 --single-branch https://github.com/easybuilders/easybuild-easyblocks.git - cd easybuild-easyblocks; git log -n 1; cd - - pip install $PWD/easybuild-easyblocks # install environment modules tool using 'install_eb_dep.sh' script provided by easybuild-framework From f16c274d5781cd6534c8f2ebd30b91cd85d72f54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 May 2020 20:12:31 +0200 Subject: [PATCH 413/431] run LAMMPS test case in easyconfig for LAMMPS 3Mar2020 using foss/2020a --- ...MMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb index 589ce20cd25..d196f9c53c6 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb @@ -21,11 +21,15 @@ toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -# See https://github.com/lammps/lammps/pull/1483 for why this is needed +sources = [ + 'stable_%(version)s.tar.gz', + {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, +] +# see https://github.com/lammps/lammps/pull/1483 for why this is needed patches = ['lammps-stable_3Mar2020_hack_openmp_gcc9.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz + '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py '41a0bcb828be22d38bb489bbd4b1fd7803d7771a2308371f01e961c52b8c869f', # lammps-stable_3Mar2020_hack_openmp_gcc9.patch ] @@ -90,4 +94,10 @@ user_packages = [ 'SCAFACOS', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', 'VTK' ] +enhance_sanity_check = True + +# run short test case to make sure installation doesn't produce blatently incorrect results; +# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b +sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] + moduleclass = 'chem' From e36751bd40b7ddd377bc945271e5c78593dbc921 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 13 May 2020 21:30:34 +0000 Subject: [PATCH 414/431] Add zlib-1.2.11 as dependecy (see #5033) --- .../easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb b/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb index 4f4ab7d6a83..1410668b13a 100644 --- a/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb +++ b/easybuild/easyconfigs/n/nifti2dicom/nifti2dicom-0.4.11-foss-2019b.eb @@ -28,6 +28,7 @@ builddependencies = [ dependencies = [ ('ITK', '5.0.1', '-Python-3.7.4'), ('TCLAP', '1.2.2'), + ('zlib', '1.2.11'), ] sanity_check_paths = { From 4aac4c78914f560ab540519abc67368970f365ae Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 14 May 2020 00:23:33 +0200 Subject: [PATCH 415/431] Use SYSTEM toolchain variable --- easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb | 2 +- easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb index fdac301b969..19857c19d59 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'system', 'version': 'system'} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb b/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb index cf06a9a8934..0b9eb8caf50 100644 --- a/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb +++ b/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb @@ -13,7 +13,7 @@ description = """ a variety of online storage services """ -toolchain = {'name': 'system', 'version': ''} +toolchain = SYSTEM source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] sources = ['%(name)s-v%(version)s-linux%(versionsuffix)s.zip'] From 055fdc1af0b142691ed69c67b11bd49cb98c5143 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Thu, 14 May 2020 17:15:37 +0200 Subject: [PATCH 416/431] Use upstream bugfix for binutils/2.31.1 --- .../easyconfigs/b/binutils/binutils-2.31.1.eb | 2 +- .../binutils/binutils-2.31.1_fix_gcc10.patch | 87 ++++++++++++++----- 2 files changed, 66 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb index 6de0335c1e6..6bfa92c993e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb @@ -19,7 +19,7 @@ checksums = [ # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch - '75bc1c8fa1b5e9be9e54bdd79bd51a33669268d26ea14136c7d58cc6cc1e52f7', # binutils-2.31.1_fix_gcc10.patch + '21db43dc787f4aac61f85ee3348bf83a1195569c5f30c02b0c832a2f6b40b1a6', # binutils-2.31.1_fix_gcc10.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch b/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch index 8721575710a..76890ca9c41 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch @@ -1,26 +1,69 @@ -Widen integer type compared to enum +From dc1f2887c513c4c2110d2d997ab33ce36b9696fc Mon Sep 17 00:00:00 2001 +From: Cary Coutant +Date: Mon, 6 Aug 2018 13:36:42 -0700 +Subject: [PATCH] Fix type checking errors. -GCC 10 seems to enforce signedness between types when comparing values. +gold/ + * target.h (Sized_target::record_gnu_property): Change first two + parameters to unsigned int. + * x86_64.cc (Target_x86_64::record_gnu_property): Likewise. +--- + gold/ChangeLog | 6 ++++++ + gold/target.h | 3 ++- + gold/x86_64.cc | 5 +++-- + 3 files changed, 11 insertions(+), 3 deletions(-) -Author: Lars Viklund -diff -ru binutils-2.31.1.orig/gold/x86_64.cc binutils-2.31.1/gold/x86_64.cc ---- binutils-2.31.1.orig/gold/x86_64.cc 2018-06-24 20:38:57.000000000 +0200 -+++ binutils-2.31.1/gold/x86_64.cc 2020-05-13 00:56:30.254725766 +0200 -@@ -1585,7 +1585,7 @@ - { - uint32_t val = 0; +diff --git a/gold/ChangeLog b/gold/ChangeLog +index d5cc02b14bd..befa832b119 100644 +--- a/gold/ChangeLog ++++ b/gold/ChangeLog +@@ -1,3 +1,9 @@ ++2018-08-06 Cary Coutant ++ ++ * target.h (Sized_target::record_gnu_property): Change first two ++ parameters to unsigned int. ++ * x86_64.cc (Target_x86_64::record_gnu_property): Likewise. ++ + 2018-07-30 Nick Clifton + + * layout.cc (section_name_mapping): Add an entry for +diff --git a/gold/target.h b/gold/target.h +index bb312067b5f..bbc87396f62 100644 +--- a/gold/target.h ++++ b/gold/target.h +@@ -1147,7 +1147,8 @@ class Sized_target : public Target + // Record a target-specific program property in the .note.gnu.property + // section. + virtual void +- record_gnu_property(int, int, size_t, const unsigned char*, const Object*) ++ record_gnu_property(unsigned int, unsigned int, size_t, ++ const unsigned char*, const Object*) + { } -- switch (pr_type) -+ switch ((size_t)(uint32_t)pr_type) - { - case elfcpp::GNU_PROPERTY_X86_ISA_1_USED: - case elfcpp::GNU_PROPERTY_X86_ISA_1_NEEDED: -@@ -1606,7 +1606,7 @@ - break; - } + // Merge the target-specific program properties from the current object. +diff --git a/gold/x86_64.cc b/gold/x86_64.cc +index 27f273d64b3..9d742f6f132 100644 +--- a/gold/x86_64.cc ++++ b/gold/x86_64.cc +@@ -1307,7 +1307,8 @@ class Target_x86_64 : public Sized_target + // Record a target-specific program property in the .note.gnu.property + // section. + void +- record_gnu_property(int, int, size_t, const unsigned char*, const Object*); ++ record_gnu_property(unsigned int, unsigned int, size_t, ++ const unsigned char*, const Object*); -- switch (pr_type) -+ switch ((size_t)(uint32_t)pr_type) - { - case elfcpp::GNU_PROPERTY_X86_ISA_1_USED: - this->isa_1_used_ |= val; + // Merge the target-specific program properties from the current object. + void +@@ -1579,7 +1580,7 @@ Target_x86_64::rela_irelative_section(Layout* layout) + template + void + Target_x86_64::record_gnu_property( +- int, int pr_type, ++ unsigned int, unsigned int pr_type, + size_t pr_datasz, const unsigned char* pr_data, + const Object* object) + { +-- +2.18.2 + From 8170041ced1358216800625dc780b0d651a1b525 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Thu, 14 May 2020 17:23:04 +0200 Subject: [PATCH 417/431] Use part of upstream bugfix for binutils/2.31.1 --- .../easyconfigs/b/binutils/binutils-2.31.1.eb | 2 +- .../b/binutils/binutils-2.31.1_fix_gcc10.patch | 17 +++-------------- 2 files changed, 4 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb index 6bfa92c993e..76de1a8590e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb @@ -19,7 +19,7 @@ checksums = [ # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch - '21db43dc787f4aac61f85ee3348bf83a1195569c5f30c02b0c832a2f6b40b1a6', # binutils-2.31.1_fix_gcc10.patch + '3148916836460c21de4735785c3c5edb71972448be8fc3feb57a83178dadbfce', # binutils-2.31.1_fix_gcc10.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch b/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch index 76890ca9c41..2221a0cb682 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1_fix_gcc10.patch @@ -1,3 +1,6 @@ +Upstream patch for the coercion errors in GCC10, update of Changelog +removed as it does not apply cleanly. + From dc1f2887c513c4c2110d2d997ab33ce36b9696fc Mon Sep 17 00:00:00 2001 From: Cary Coutant Date: Mon, 6 Aug 2018 13:36:42 -0700 @@ -13,20 +16,6 @@ gold/ gold/x86_64.cc | 5 +++-- 3 files changed, 11 insertions(+), 3 deletions(-) -diff --git a/gold/ChangeLog b/gold/ChangeLog -index d5cc02b14bd..befa832b119 100644 ---- a/gold/ChangeLog -+++ b/gold/ChangeLog -@@ -1,3 +1,9 @@ -+2018-08-06 Cary Coutant -+ -+ * target.h (Sized_target::record_gnu_property): Change first two -+ parameters to unsigned int. -+ * x86_64.cc (Target_x86_64::record_gnu_property): Likewise. -+ - 2018-07-30 Nick Clifton - - * layout.cc (section_name_mapping): Add an entry for diff --git a/gold/target.h b/gold/target.h index bb312067b5f..bbc87396f62 100644 --- a/gold/target.h From 0902395f31d72062b10fd9473452b49c815384a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 May 2020 09:30:53 +0200 Subject: [PATCH 418/431] replace /path/to with actual installation prefix in FuSeq scripts --- easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb b/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb index 32cd982ff69..2f064bc71dc 100644 --- a/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb +++ b/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb @@ -45,7 +45,13 @@ preconfigopts = "cp -a %(builddir)s/FuSeq-%(version)s/{include,src} %(builddir)s # build fails otherwise parallel = 1 -postinstallcmds = ["cp -a %(builddir)s/FuSeq-%(version)s/{createAnno,R} %(installdir)s/"] +postinstallcmds = [ + # copy createAnno and R subdirectories as well + "cp -a %(builddir)s/FuSeq-%(version)s/{createAnno,R} %(installdir)s/", + # replace /path/to with installation prefix in scripts + "sed -i 's@/path/to/@%(installdir)s/R/@' %(installdir)s/R/FuSeq.R", + "ls %(installdir)s/createAnno/*.sh | xargs sed -i 's@/path/to/FuSeq_home/@%(installdir)s/@'", +] sanity_check_paths = { 'files': ['bin/FuSeq', 'bin/GenTC', 'bin/TxIndexer', 'lib/libsailfish_core.a', 'R/FuSeq.R'], From bcd4b5be05ff029a11ec4e55fb9cd5d81bb2c497 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 May 2020 11:10:49 +0200 Subject: [PATCH 419/431] adding easyconfigs: rickflow-0.7.0-intel-2019b-Python-3.7.4.eb --- ...rickflow-0.7.0-intel-2019b-Python-3.7.4.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..2a8891a4f82 --- /dev/null +++ b/easybuild/easyconfigs/r/rickflow/rickflow-0.7.0-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'rickflow' +version = '0.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gitlab.com/Olllom/rickflow' +description = "Running and Analyzing OpenMM Jobs" + +toolchain = {'name': 'intel', 'version': '2019b'} + + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('PyYAML', '5.1.2'), + ('MDTraj', '1.9.3', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('OpenMM', '7.4.1', versionsuffix), + ('netcdf4-python', '1.5.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('mpiplus', '0.0.1', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/choderalab/mpiplus/archive/'], + 'checksums': ['a3d50157a274decab87589ad78b9e41e9f3d34eb27a7d50cc6e7ef34def98b44'], + }), + ('pymbar', '3.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], + }), + ('openmmtools', '0.19.0', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/choderalab/openmmtools/archive/'], + 'checksums': ['32f74d9ff9d3897d907b57ae1480929dd3ef29918cf82da13a2a2d6f74d5eeb8'], + }), + (name, version, { + 'modulename': 'rflow', + 'source_urls': ['https://gitlab.com/Olllom/%(name)s/-/archive/%(version)s/'], + 'checksums': ['132f0e5a960a2ed1eb49afd18d73cb6d66367a236084e7db89699b252408cb52'], + }), +] + +sanity_check_paths = { + 'files': ['bin/rflow'], + 'dirs': [], +} + +sanity_check_commands = ["rflow --help"] + +sanity_pip_check = True + +moduleclass = 'chem' From 82f567bfa97f5cb1a332e721af4b4f60db7ab6f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 May 2020 11:55:53 +0200 Subject: [PATCH 420/431] adding easyconfigs: HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb, KMC-3.1.2rc1-GCC-8.3.0-Python-3.7.4.eb, SDSL-2.1.1-20191211-GCC-8.3.0.eb --- .../HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb | 40 ++++++++++++++++ .../KMC-3.1.2rc1-GCC-8.3.0-Python-3.7.4.eb | 44 +++++++++++++++++ .../s/SDSL/SDSL-2.1.1-20191211-GCC-8.3.0.eb | 47 +++++++++++++++++++ 3 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.1.2rc1-GCC-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/s/SDSL/SDSL-2.1.1-20191211-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..5d84f8de4eb --- /dev/null +++ b/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'HyPo' +version = '1.0.3' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://github.com/kensung-lab/hypo' +description = "HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/kensung-lab/%(namelower)s/releases/download/v1.0.3'] +sources = ['%(namelower)s-v1.0.3.tar.gz'] +checksums = ['f936069830b8a1dbd8d9825593b35ee83fc891c0419c395b2f2c858f329b3810'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('zlib', '1.2.11'), + ('KMC', '3.1.2rc1', versionsuffix), + ('HTSlib', '1.10.2'), + ('SDSL', '2.1.1-20191211'), +] + +preconfigopts = "rm -r %(builddir)s/hypo*/external/install/htslib/lib && " + +# FIXME check whether this is really needed +configopts = "-Doptimise_for_native=ON " + +# using 'Conda' as build type to make CMake honor the specified location for dependencies +configopts += "-DCMAKE_BUILD_TYPE=Conda -DHTSLIB_INSTALL_DIR=$EBROOTHTSLIB -DSDSLLIB_INSTALL_DIR=$EBROOTSDSL" + +sanity_check_paths = { + 'files': ['bin/hypo'], + 'dirs': [], +} + +sanity_check_commands = ["hypo --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.1.2rc1-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/k/KMC/KMC-3.1.2rc1-GCC-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..82ca85efc35 --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.1.2rc1-GCC-8.3.0-Python-3.7.4.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'KMC' +version = '3.1.2rc1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sun.aei.polsl.pl/kmc' +description = "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/refresh-bio/KMC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a1958c4f3c6fd7c7ebb8b478c00fce1fd0f328c634042f723c5917a9d030a3fe'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('Python', '3.7.4'), +] + +# Makefile does static linking with libc.a, libpthread.a, libm.a +osdependencies = [('glibc-static', 'libc6-dev')] + +prebuildopts = "sed -i 's@[^ ]*/libz.a@${EBROOTZLIB}/lib/libz.a@g' makefile && " +prebuildopts += "sed -i 's@[^ ]*/libbz2.a@${EBROOTBZIP2}/lib/libbz2.a@g' makefile && " + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/kmc_dump'], + 'dirs': [], +} + +sanity_check_commands = [ + "kmc", + "kmc_dump", + "python -c 'import py_kmc_api'", +] + +# Python bindings are also located in bin/ +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SDSL/SDSL-2.1.1-20191211-GCC-8.3.0.eb b/easybuild/easyconfigs/s/SDSL/SDSL-2.1.1-20191211-GCC-8.3.0.eb new file mode 100644 index 00000000000..93ea19af749 --- /dev/null +++ b/easybuild/easyconfigs/s/SDSL/SDSL-2.1.1-20191211-GCC-8.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'SDSL' +version = '2.1.1-20191211' + +homepage = 'https://github.com/simongog/sdsl-lite' +description = """The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing + succinct data structures.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/simongog/sdsl-lite/archive/'] +sources = [ + { + 'download_filename': 'c32874c.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/google/googletest/archive/'], + 'download_filename': 'release-1.10.0.tar.gz', + 'filename': 'googletest-1.10.0.tar.gz', + }, + { + 'source_urls': ['https://github.com/simongog/libdivsufsort/archive/'], + 'download_filename': '22e6b23.tar.gz', + 'filename': 'libdivsufsort-2.0.1-20161201.tar.gz', + }, +] +checksums = [ + 'ffab55af40d33a1a1705a693589d95ec31318270d58830a00d3723ee74b0c47b', # SDSL-2.1.1-20191211.tar.gz + '9dc9157a9a1551ec7a7e43daea9a694a0bb5fb8bec81235d8a1e6ef64c716dcb', # googletest-1.10.0.tar.gz + '211d4c64c13175a5020f4f16e418b9410facf5d22fb2cb7295a58887a61ae13f', # libdivsufsort-2.0.1-20161201.tar.gz +] + +builddependencies = [('CMake', '3.15.3')] + +preconfigopts = "cp -a %(builddir)s/googletest-*/* %(builddir)s/sdsl-lite-*/external/googletest/ && " +preconfigopts += "cp -a %(builddir)s/libdivsufsort-*/* %(builddir)s/sdsl-lite-*/external/libdivsufsort/ && " + +configopts = "-DBUILD_GMOCK=OFF -DINSTALL_GTEST=OFF" + +sanity_check_paths = { + 'files': ['lib/libsdsl.a'], + 'dirs': ['include/sdsl'], +} + +moduleclass = 'lib' From 26fe436c08a32345a244fab80fde7c5b22b0995f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 15 May 2020 20:52:03 +0200 Subject: [PATCH 421/431] Update easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb --- easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb index 47a7c64dc74..dbdc0cfae2d 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-foss-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Stacks' version = '2.53' -homepage = 'http://catchenlab.life.illinois.edu/stacks/' +homepage = 'https://catchenlab.life.illinois.edu/stacks/' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. From 1b1f53900017385b4b2491279b9073c8123734e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 May 2020 16:13:12 +0200 Subject: [PATCH 422/431] adding easyconfigs: worker-1.6.12-foss-2019a.eb --- .../w/worker/worker-1.6.12-foss-2019a.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb new file mode 100644 index 00000000000..af9f61a3831 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb @@ -0,0 +1,89 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.12' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['503ad9db78d949999bd5f3ba15b18f746cad2eaf2ff49240398b2b6792f9ffbd'] + +osdependencies = ['perl'] + +local_tcname = 'foss' +local_tcver = '2019a' +builddependencies = [(local_tcname, local_tcver)] +versionsuffix = '-%s-%s' % (local_tcname, local_tcver) + +exts_defaultclass = 'PerlModule' + +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB/'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Text::CSV', '2.00', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], + }), + ('DBI', '1.643', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + }), + ('DBD::SQLite', '1.64', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['f4ae8f7b50842305566aadd90f7bfd12a9e32b6c603a9b1c1529e73eb82aff01'], + }), + ('Date::Language', '2.32', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC/'], + 'checksums': ['34eca099e375e2d142ea6cc935922c4980dc21c65ce7c24823ca08457c4bb3d6'], + }), + ('Template', '3.008', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['52400f68bef6731b0fca00e3438ed835b29ab9fec72a404866dee8fc139da692'], + }), +] + +preconfigopts = "export CC=mpicc && " + +modextrapaths = { + 'PERL5LIB': ['share/perl5', 'lib64/perl5'], +} + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['dbilogstrip', 'dbiprof', 'dbiproxy', 'tpage', 'ttree', 'wcat', 'wconvert', + 'wload', 'worker', 'wreduce', 'wresume', 'wsub', 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt', 'lib64/perl5'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From f6a3c29a0503c483f83b69f278560972073093f9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 May 2020 13:25:27 +0200 Subject: [PATCH 423/431] adding easyconfigs: GROMACS-2020.1-foss-2020a-Python-3.8.2.eb and patches: GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch, GROMACS-2020.1_dont_override_pythonpath_in_tests.patch, gmxapi-0.1.0.1_drop_cmake_requirement.patch --- .../GROMACS-2020.1-foss-2020a-Python-3.8.2.eb | 96 +++++++++++++++++++ ....1_dont_override_pythonpath_in_tests.patch | 15 +++ ...2020_fix_gmxapi_gmx_allowed_cmd_name.patch | 39 ++++++++ ...mxapi-0.1.0.1_drop_cmake_requirement.patch | 16 ++++ 4 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch create mode 100644 easybuild/easyconfigs/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..2cc942771df --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,96 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# License:: MIT/GPL +# 2019.3 version +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# + +name = 'GROMACS' +version = '2020.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', + 'GROMACS-%(version)s_dont_override_pythonpath_in_tests.patch', + 'GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch', +] +checksums = [ + 'e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf', # gromacs-2020.1.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', + # GROMACS-2020.1_dont_override_pythonpath_in_tests.patch + 'dffcafefeb594864c452cbeea3ee13091168c7ab9cd1f63dc8e9d1663dcb928e', + # GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch + '564c4e97e0dd05df1f45415ab5cc755c6b157880b26a816f7d6f7f98b318c900', +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('scikit-build', '0.10.0', versionsuffix), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('networkx', '2.4', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.1.0.1', { + 'patches': ['gmxapi-0.1.0.1_drop_cmake_requirement.patch'], + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': [ + '3371075975117a32ffe44e8972a4a9330da416f0054e00ee587cdffb217497a0', # gmxapi-0.1.0.1.tar.gz + # gmxapi-0.1.0.1_drop_cmake_requirement.patch + 'c58f1d94e7681bb2931ac90929445dc90f1709a9d8d3be78e55adbda797a2e8c', + ], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch new file mode 100644 index 00000000000..8b0bdd51a25 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.1_dont_override_pythonpath_in_tests.patch @@ -0,0 +1,15 @@ +Don't overwrite PYTHONPATH when executing tests, add to it instead. + +Åke Sandgren, 20200309 +diff -ru gromacs-2020.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2020.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt +--- gromacs-2020.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2020-03-03 17:24:49.000000000 +0100 ++++ gromacs-2020.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2020-03-09 09:18:42.707693465 +0100 +@@ -22,7 +22,7 @@ + get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir) + get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY) + add_custom_target(gmxapi_extension_pytest +- COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR} ++ COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR} + ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} + DEPENDS gmxapi_extension _gmxapi + WORKING_DIRECTORY ${PLUGINPATH}) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch new file mode 100644 index 00000000000..ad6ee3c07f5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch @@ -0,0 +1,39 @@ +Fix search for "gmx" binary to allow for double precision builds. + +Åke Sandgren, 20200318 +diff -ru gromacs-2020.1.orig/python_packaging/sample_restraint/tests/conftest.py gromacs-2020.1/python_packaging/sample_restraint/tests/conftest.py +--- gromacs-2020.1.orig/python_packaging/sample_restraint/tests/conftest.py 2020-03-03 17:24:49.000000000 +0100 ++++ gromacs-2020.1/python_packaging/sample_restraint/tests/conftest.py 2020-03-18 07:19:09.611507575 +0100 +@@ -156,7 +156,7 @@ + # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary. + # We should be able to get the GMXRC contents and related hints from a gmxapi + # package resource or from module attributes of a ``gromacs`` stub package. +- allowed_command_names = ['gmx', 'gmx_mpi'] ++ allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']] + command = None + for command_name in allowed_command_names: + if command is not None: +diff -ru gromacs-2020.1.orig/python_packaging/src/test/conftest.py gromacs-2020.1/python_packaging/src/test/conftest.py +--- gromacs-2020.1.orig/python_packaging/src/test/conftest.py 2020-03-03 17:24:49.000000000 +0100 ++++ gromacs-2020.1/python_packaging/src/test/conftest.py 2020-03-18 07:19:27.535301581 +0100 +@@ -156,7 +156,7 @@ + # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary. + # We should be able to get the GMXRC contents and related hints from a gmxapi + # package resource or from module attributes of a ``gromacs`` stub package. +- allowed_command_names = ['gmx', 'gmx_mpi'] ++ allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']] + command = None + for command_name in allowed_command_names: + if command is not None: +diff -ru gromacs-2020.1.orig/python_packaging/test/conftest.py gromacs-2020.1/python_packaging/test/conftest.py +--- gromacs-2020.1.orig/python_packaging/test/conftest.py 2020-03-03 17:24:49.000000000 +0100 ++++ gromacs-2020.1/python_packaging/test/conftest.py 2020-03-18 07:19:03.967572439 +0100 +@@ -156,7 +156,7 @@ + # TODO: (#2896) Find a more canonical way to identify the GROMACS commandline wrapper binary. + # We should be able to get the GMXRC contents and related hints from a gmxapi + # package resource or from module attributes of a ``gromacs`` stub package. +- allowed_command_names = ['gmx', 'gmx_mpi'] ++ allowed_command_names = ['gmx%s%s' % (m, p) for m in ['', '_mpi'] for p in ['', '_d']] + command = None + for command_name in allowed_command_names: + if command is not None: diff --git a/easybuild/easyconfigs/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch b/easybuild/easyconfigs/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch new file mode 100644 index 00000000000..57e5e610f6c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/gmxapi-0.1.0.1_drop_cmake_requirement.patch @@ -0,0 +1,16 @@ +Drop the cmake requirement from gmxapi, we take that from the dependencies list. + +Åke Sandgren, 20200308 +diff -ru gmxapi-0.1.0.1.orig/setup.py gmxapi-0.1.0.1/setup.py +--- gmxapi-0.1.0.1.orig/setup.py 2019-12-30 12:08:34.000000000 +0100 ++++ gmxapi-0.1.0.1/setup.py 2020-03-08 17:00:54.456270981 +0100 +@@ -152,8 +152,7 @@ + # TODO: (pending infrastructure and further discussion) Replace with CMake variables from GMXAPI version. + version='0.1.0.1', + python_requires='>=3.5, <3.9', +- setup_requires=['cmake>=3.12', +- 'setuptools>=28', ++ setup_requires=['setuptools>=28', + 'scikit-build>=0.7'], + + packages=['gmxapi', 'gmxapi.simulation'], From 59ce6a45db452b27cb6a250b4605cc19310e72d6 Mon Sep 17 00:00:00 2001 From: Marco Verdicchio Date: Tue, 19 May 2020 18:25:16 +0200 Subject: [PATCH 424/431] adding easyconfigs: ADF-2019.303-intelmpi.eb --- .../a/ADF/ADF-2019.303-intelmpi.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/a/ADF/ADF-2019.303-intelmpi.eb diff --git a/easybuild/easyconfigs/a/ADF/ADF-2019.303-intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2019.303-intelmpi.eb new file mode 100755 index 00000000000..2e7641ae373 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2019.303-intelmpi.eb @@ -0,0 +1,34 @@ +easyblock = 'Tarball' + +name = 'ADF' +version = '2019.303' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/ADF/' +description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and + predict chemical structure and reactivity with density functional theory (DFT).""" + +toolchain = SYSTEM + +sources = ['adf%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['62f73d2bc37bfc7891c1b10e83abccae317f7751f2a7b88976b24d16ef2b771a'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextravars = { + 'ADFHOME': '%(installdir)s', + 'ADFBIN': '%(installdir)s/bin', + 'ADFRESOURCES': '%(installdir)s/atomicdata', +} + +modloadmsg = """These environment variables need to be defined before using ADF: + * $SCMLICENSE: path to ADF license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From d18764aea9f762748ae738fc4651a68a59082de4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 May 2020 19:52:40 +0200 Subject: [PATCH 425/431] Whitelist updated Amber versions that are missing -Python suffix --- test/easyconfigs/easyconfigs.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index cd36e0cc23b..250eb59a34d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -421,9 +421,11 @@ def check_python_packages(self, changed_ecs): if exts_default_options.get(key) is None: failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) + whitelist_python_suffix = ['Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] # if Python is a dependency, that should be reflected in the versionsuffix # Tkinter is an exception, since its version always matches the Python version anyway - if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter': + if any(dep['name'] == 'Python' for dep in ec['dependencies']) and + ec.name != 'Tkinter' and not any(re.match(regex, ec_fn) for regex in whitelist_python_suffix): if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) From 6c7a0561d2918a6c780cfcc11a226885089ac4ec Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 May 2020 20:00:55 +0200 Subject: [PATCH 426/431] Adjust code for checking -Python suffix to make it easier to read --- test/easyconfigs/easyconfigs.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 05a1f19e95b..a61d2dbe420 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -595,11 +595,13 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): if exts_default_options.get(key) is None: failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) - whitelist_python_suffix = ['Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] # if Python is a dependency, that should be reflected in the versionsuffix # Tkinter is an exception, since its version always matches the Python version anyway - if any(dep['name'] == 'Python' for dep in ec['dependencies']) and - ec.name != 'Tkinter' and not any(re.match(regex, ec_fn) for regex in whitelist_python_suffix): + # Also whitelist some updated versions of Amber + whitelist_python_suffix = ['Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] + whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix): + has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies']) + if has_python_dep and ec.name != 'Tkinter' and not whitelisted: if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): msg = "'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn # This is only a failure for newly added ECs, not for existing ECS From d7c3e2a9318e3f6e53c66f08a261626aac845245 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 May 2020 20:03:50 +0200 Subject: [PATCH 427/431] Fix typo in whitelist checking for -Python suffix --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a61d2dbe420..894377797d1 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -599,7 +599,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): # Tkinter is an exception, since its version always matches the Python version anyway # Also whitelist some updated versions of Amber whitelist_python_suffix = ['Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] - whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix): + whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies']) if has_python_dep and ec.name != 'Tkinter' and not whitelisted: if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): From 2cdd82346c2601026d46859081ce2f792778eabf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 May 2020 22:26:49 +0200 Subject: [PATCH 428/431] adding easyconfigs: TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb --- ...ensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb | 142 ++++++++++++++++++ 1 file changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..9fce463ed35 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,142 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [ + ('Bazel', '2.0.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + # For SciPy + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +exts_list = [ + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('pyasn1-modules', '0.2.8', { + 'modulename': 'pyasn1_modules', + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.0', { + 'checksums': ['1a836406405730121ae9823e19c6e806c62bbad73f890574fff50efa4122c487'], + }), + ('cachetools', '4.1.0', { + 'checksums': ['1d057645db16ca7fe1f3bd953558897603d6f0b9c51ed9d11eb4d071ec4e2aab'], + }), + ('google-auth', '1.14.2', { + 'modulename': 'google.auth', + 'checksums': ['2243db98475f7f2033c41af5185333cbf13780e8f5f96eaadd997c6f34181dcc'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'modulename': 'requests_oauthlib', + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.1', { + 'modulename': 'google_auth_oauthlib', + 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('protobuf', '3.11.3', { + 'modulename': 'google.protobuf', + 'checksums': ['c77c974d1dadf246d789f6dad1c24426137c9091e930dbf50e0a29c1fcf00b1f'], + }), + ('absl-py', '0.9.0', { + 'modulename': 'absl', + 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.28.1', { + 'modulename': 'grpc', + 'checksums': ['cbc322c5d5615e67c2a15be631f64e6c2bab8c12505bc7c150948abdaa0bdbac'], + }), + ('tensorboard-plugin-wit', '1.6.0.post3', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['1fdf4ac343f1665453205aef8bb227b0204893bb5ffb792d2ed4509b1daf3d4f'], + }), + ('tensorboard', '2.2.1', { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['9a2a2dc9856187679e93f3c95e5dc771dd47e3257db09767b4be118d734b4dc2'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.2.1', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['83b76a98d18ae6a5cc7a0d88955a7f74881f0e567a0f4c949d24c942753eb998'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.0', { + 'modulename': 'keras_preprocessing', + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-1.14.0_swig-env.patch', + 'TensorFlow-1.14.0_remove_usrbin_from_linker_bin_path_flag.patch', + 'TensorFlow-2.1.0_fix-cuda-build.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + '69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3', # v2.2.0.tar.gz + 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', # TensorFlow-1.14.0_swig-env.patch + # TensorFlow-1.14.0_remove_usrbin_from_linker_bin_path_flag.patch + 'bfa2701495dddfbbf4fbec808ea3c982b50043a16d28a8d1283f44df0b8aae7d', + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + ], + }), +] + +moduleclass = 'lib' From 2ce3342cbdd36efc08d107ba67a51defe8cb808a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 May 2020 14:01:40 +0800 Subject: [PATCH 429/431] prepare release notes for eb421 --- RELEASE_NOTES | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 80 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index ffd38901557..14d6f493b71 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,9 +3,88 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 9,462 easyconfig files, for 1,912 different software packages, +The latest version of easybuild-easyconfig provides 9,898 easyconfig files, for 1,978 different software packages, incl. 31 different (compiler) toolchains. +v4.2.1 (May 20th 2020) +---------------------- + +update/bugfix release + +- added example easyconfig files for 66 new software packages: + - Alpha (#9994), Arlequin (#10620), AutoMap (#10419), antiSMASH (#10589), artic-ncov2019 (#10459), augur (#10405), + Bio-EUtilities (#10037), CaSpER (#10593), CoCoALib (#10429), cdbfasta (#10547), cddlib (#10429), + DoubletFinder (#10603), dftd3-lib (#10351), E-ANTIC (#10429), FIX (#8870), FastViromeExplorer (#10571), + FusionCatcher (#10134), geopandas (#10322), goalign (#10469), gotree (#10459), gretl (#10413), HDF-EOS (#10534), + HDF-EOS5 (#10536), HMMER2 (#10588), HyPo (#10642), harmony (#10604), king (#10365), libdeflate (#10459), + libfabric (#10616), libgit2 (#10453), libuv (#10444), MDAnalysis (#10545), MEM (#10605), MESS (#10597), + MinCED (#10037), MitoZ (#7735), mbuffer (#10524), metaerg (#10037), NLMpy (#10029), NTL (#10431), nauty (#10429), + nifti2dicom (#10598), ntCard (#10502), ProtHint (#10549), PyVCF (#10564), PyWavelets (#10501), pIRS (#10508), + popscle (#10550), protozero (#10495), pysndfx (#10452), RNA-Bloom (#10502), rampart (#10459), rickflow (#10641), + root_numpy (#10424), rstudio (#10619), SDSL (#10642), SHAP (#10379), SNPomatic (#10524), ScaFaCoS (#10537), + Scythe (#10524), SoX (#10452), swissknife (#10037),) TCLAP (#10598), Taiyaki (#10573), torchaudio (#10516), + wtdbg2 (#10524) +- added additional easyconfigs for various supported software packages, including: + - 4ti2 1.6.9, ADF 2019.303, ARAGORN 1.2.38, ATK 2.36.0, AUGUSTUS 3.3.3, Alpha 20200430, Anaconda3 2020.02.eb, Arb 2.16.0, Arlequin 3.5.2.2, ArviZ 0.7.0, AutoMap 1.0, Autoconf 2.69, Automake 1.16.1, Autotools 20180311, angsd 0.933, angsd 0.933, antiSMASH 5.1.2, archspec 0.1.0, artic ncov2019, at spi2, at spi2, attr 2.4.48, augur 7.0.2, BBMap 38.79, BCFtools 1.10.2, BRAKER 2.1.5, BWA 0.7.17, Bazel 2.0.0, Bio EUtilities, Biopython 1.75, Bison 3.6.1, Blosc 1.17.1, Bonito 0.1.4, Boost.Python 1.72.0, Boost.Python 1.72.0, Boost 1.72.0, Boost 1.72.0, Bowtie 1.2.3, Bowtie2 2.4.1, bcl2fastq2 2.20.0, binutils 2.34, bzip2 1.0.8, CITE seq, CLISP 2.49, CMake 3.16.4, CPLEX 12.10, CVXOPT 1.2.4, CaSpER 2.0, CoCoALib 0.99601, Coreutils 8.32, CubeLib 4.4.4, CubeWriter 4.4.3, cURL 7.69.1, cairo 1.16.0, cdbfasta 0.99, cdbfasta 0.99, cdbfasta 0.99, cddlib 0.94i, csvkit 1.0.5, ctffind 4.1.13, DB 18.1.32, DBus 1.13.12, DCMTK 3.6.5, DFTB+ 19.1, DFTB+ 19.1, DoubletFinder 2.0.3, Doxygen 1.8.17, dftd3 lib, double conversion, E ANTIC, ETE 3.1.1, EasyBuild 4.2.0.eb, Eigen 3.3.7, Exonerate 2.4.0, ecCodes 2.17.0, ecCodes 2.17.0, expat 2.2.9, FFTW 3.3.8, FFTW 3.3.8, FFmpeg 4.2.2, FIX 1.06.12, FLASH 1.2.11, FLINT 2.5.2, FSL 6.0.2, FSL 6.0.2, FastViromeExplorer 20180422, FriBidi 1.0.9, FusionCatcher 1.20, file 5.38, flex 2.6.4, fontconfig 2.13.92, foss 2020a.eb, freetype 2.10.1, GATK 4.1.5.0, GCC 10.1.0.eb, GCC 9.3.0.eb, GCCcore 10.1.0.eb, GDAL 3.0.4, GDAL 3.0.4, GDCM 3.0.5, GEOS 3.8.1, GEOS 3.8.1, GLPK 4.65, GLib 2.64.1, GMP 6.2.0, GObject Introspection, GROMACS 2020.1, GSL 2.6, GSL 2.6, GST plugins, GStreamer 1.16.2, GTK+ 3.24.17, Gdk Pixbuf, GeneMark ET, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GitPython 3.1.0, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2, GlobalArrays 5.7.2, Guile 1.8.8, gap 4.11.0, gc 7.6.12, geopandas 0.7.0, gettext 0.20.1, gflags 2.2.2, glew 2.1.0, glew 2.1.0, glog 0.4.0, gmpy2 2.1.0b4, gmsh 4.5.6, gnuplot 5.2.8, goalign 0.3.2.eb, gompi 2020a.eb, gotree 0.4.0.eb, gperf 3.1, gpustat 0.6.0, gradunwarp 1.2.0, gradunwarp 1.2.0, gretl 2020a, gzip 1.10, HDDM 0.7.5, HDF EOS, HDF EOS5, HDF5 1.10.6, HDF5 1.10.6, HMMER2 2.3.2, HPL 2.3, HPL 2.3, HTSlib 1.10.2, HarfBuzz 2.6.4, HyPo 1.0.3, Hypre 2.18.2, Hypre 2.18.2, h5py 2.10.0, harmony 1.0.0, help2man 1.47.15, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1, IPython 7.13.0, IPython 7.13.0, IQ TREE, ImageMagick 7.0.10, iccifort 2020.1.217.eb, iimpi 2020a.eb, imkl 2020.1.217, impi 2019.7.217, intel 2020a.eb, intltool 0.51.0, JasPer 2.0.14, Julia 1.4.1, jbigkit 2.1, KMC 3.1.2rc1, Kraken2 2.0.9, kim api, kim api, king 2.2.4.eb, LAME 3.100, LAMMPS 3Mar2020, LLVM 9.0.1, LMDB 0.9.24, LMfit 1.0.0, LZO 2.10, LZO 2.10, LibTIFF 4.1.0, LittleCMS 2.9, Longshot 0.4.1, Lua 5.3.5, libGLU 9.0.1, libarchive 3.4.2, libcerf 1.13, libcroco 0.6.13, libdeflate 1.5, libdrm 2.4.100, libepoxy 1.5.4, libevent 2.1.11, libfabric 1.10.1, libfabric 1.9.1, libffcall 2.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libgeotiff 1.5.1, libgit2 1.0.0, libglvnd 1.2.0, libjpeg turbo, libmatheval 1.1.11, libpciaccess 0.16, libpng 1.6.37, libreadline 8.0, librsvg 2.48.4, libsigsegv 2.12, libsndfile 1.0.28, libsodium 1.0.18, libtool 2.4.6, libunistring 0.9.10, libunwind 1.3.1, libuv 1.37.0, libxc 4.3.4, libxml2 2.9.10, libyaml 0.2.2, lpsolve 5.5.2.5, lrslib 7.0a, lz4 1.9.2, M4 1.4.18, MAFFT 7.427, MDAnalysis 0.20.1, MDAnalysis 0.20.1, MDTraj 1.9.3, MEM 20191023, MEM 20191023, MEME 5.1.1, MEME 5.1.1, MESS 0.1.6, METIS 5.1.0, MPC 1.1.0, MPFR 4.0.2, MUMPS 5.2.1, MUMPS 5.2.1, MUSCLE 3.8.31, Mako 1.1.2, MariaDB connector, Mesa 20.0.2, Meson 0.53.2, MinCED 0.4.2, MinPath 1.4, MitoZ 2.3, MotionCor2 1.3.1, MultiQC 1.8, MultiQC 1.8, Multiwfn 3.6, matplotlib 3.2.1, matplotlib 3.2.1, mbuffer 20191016, metaerg 1.2.3, minimap2 2.17, minimap2 2.17, molmod 1.4.5, molmod 1.4.5, NASM 2.14.02, NCIPLOT 4.0, NGS Python, NGS 2.10.4, NLMpy 0.1.5, NLopt 2.6.1, NSPR 4.25, NSS 3.51, NTL 11.3.4, NWChem 7.0.0, Nextflow 20.04.1.eb, Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, nauty 2.6r12, nauty 2.7rc2, ncbi vdb, ncdf4 1.17, ncurses 6.2, netCDF C++4, netCDF Fortran, netCDF Fortran, netCDF 4.7.4, netCDF 4.7.4, netMHCIIpan 3.2, netcdf4 python, networkx 2.2, networkx 2.4, nifti2dicom 0.4.11, nodejs 12.16.1, ntCard 1.2.1, numactl 2.0.13, numexpr 2.6.5, numexpr 2.7.1, numexpr 2.7.1, OPARI2 2.0.5, OTF2 2.2, OpenBLAS 0.3.9, OpenEXR 2.4.1, OpenMPI 4.0.3, OpenPGM 5.2.122, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PDT 3.25, PETSc 3.12.4, PETSc 3.12.4, PLINK 2.00a2.3_x86_64.eb, PLUMED 2.6.0, PLUMED 2.6.0, PMIx 3.1.5, PROJ 7.0.0, Pango 1.44.7, Perl 5.30.2, Pillow 7.0.0, ProtHint 2.4.0, ProtHint 2.4.0, PyMC3 3.8, PyTables 3.4.4, PyTables 3.6.1, PyTables 3.6.1, PyVCF 0.6.8, PyWavelets 1.1.1, PyYAML 5.3, Python 2.7.18, Python 3.8.2, pIRS 2.0.2, parallel 20200422, patchelf 0.10, pixman 0.38.4, pkg config, pkgconfig 1.5.1, popscle 0.1, protobuf python, protozero 1.6.8, pybind11 2.4.3, pysndfx 0.3.6, python Levenshtein, Qt5 5.14.1, QuantumESPRESSO 6.5, R bundle, R 3.6.3, R 4.0.0, RMBlast 2.9.0, RNA Bloom, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, Rust 1.42.0, Rust 1.42.0, rampart 1.2.0rc3, re2c 1.3, rickflow 0.7.0, rioxarray 0.0.24, root_numpy 4.8.0, rootpy 1.0.1, rstudio 1.2.5033, rstudio 1.2.5042, SAMtools 1.10, SCOTCH 6.0.9, SCOTCH 6.0.9, SCons 3.1.2, SDL2 2.0.10, SDSL 2.1.1, SHAP 0.35.0, SIONlib 1.7.6, SLATEC 4.1, SNPomatic 1.0, SQLite 3.31.1, SRA Toolkit, SRA Toolkit, SWIG 4.0.1, Salmon 1.2.0, ScaFaCoS 1.0.1, ScaFaCoS 1.0.1, ScaLAPACK 2.1.0, SciPy bundle, SciPy bundle, Score P, Scythe 0.994, SeqAn 2.4.0, Singular 4.1.2, SoX 14.4.2, Stacks 2.53, StringTie 2.1.1, SuiteSparse 5.7.1, SuiteSparse 5.7.1, Szip 2.1.1, scikit build, snappy 1.1.8, spaln 2.4.03, swissknife 1.80, sympy 1.5.1, TCLAP 1.2.2, Taiyaki 5.0.1, Taiyaki 5.0.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2, tbb 2020.1, tbl2asn 20200302, torchaudio 0.5.0, torchaudio 0.5.0, torchtext 0.5.0, torchvision 0.5.0, UCX 1.8.0, UDUNITS 2.2.26, UMI tools, utf8proc 2.5.0, util linux, VCFtools 0.1.16, VCFtools 0.1.16, VTK 8.2.0, VTK 8.2.0, Voro++ 0.4.6, worker 1.6.12, wtdbg2 2.5, wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, xorg macros, YAXT 0.6.2, YAXT 0.6.2, Yasm 1.3.0, yaff 1.6.0, ZeroMQ 4.3.2, zlib 1.2.11, zsh 5.8, zstd 1.4.4 +- added easyconfigs for new common toolchains: foss/2020a (#10483), intel/2020a (#10494) +- minor enhancements, including: + - add mRMRe and dHSIC and sync easyconfig in fosscuda for R v3.6.2 (#10359) + - add Mozilla::CA, Test::RequiresInternet and LWP::Protocol::https extensions to Perl 5.30.x (#10412) + - update extensions in Python 3.8.2 easyconfig (#10456) + - include LLVM linker in Clang 7.0.1 on GCC 7.3.0-2.30(#10458) + - include static lib and header in nimimap2 easyconfigs for foss-2018b and GCC-8.2.0* (#10464) + - add UCX 1.8.0 as dep for OpenMPI 4.0.3 using in foss/2020a (+ easyconfig for libfabric 1.9.1) (#10492) + - add MCE::Mutex extension to Perl 5.28.1 + 5.30.x (#10546) + - add additional extensions to R 3.6.2 + R-bundle-Bioconductor 3.10 easyconfigs (#10585) + - add additional extensions to R 3.6.3 & R 4.0.0 extensions (#10586) + - add diffcyt extension to R-bundle-Bioconductor 3.10 (#10596) + - add alternate checksum for EMBOSS (#10607) + - update ALL, pRolocdata and geneLenDataBase extensions in Bioconductor/3.11 (#10614) + - add extensions to R 4.0.0 and Bioconductor 3.11 easyconfigs (#10621) + - add additional extensions to Perl-5.30.2 easyconfig (#10623) +- various bug fixes, including: + - fix incorrect checksums for Amber patches (#8870) + - add patches to fix installation of R 3.6.2 on POWER (#9830) + - add system dependencies on ibverbs and remove UCX dependency in libfabric v1.9.1 (#10281) + - add missing build dep. pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (#10380) + - check sdist with different python versions (#10388) + - add Perl as a build dependency for Autoconf/Automake on GCCcore/8.3.0(#10408) + - add patch for AutoMap to avoid that it to create a log file in installation directory (#10414) + - fix source_urls in ICU easyconfigs (#10417) + - disable USER-INTEL package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results (#10418) + - fix undefined reference to 'qfloat16::mantissatable' in Qt5-5.13.1-GCCcore-8.3.0 (#10425) + - add Perl build dep for Autoconf/Automake using GCCcore/7.3.0 and GCCcore/8.2.0 toolchains (#10426) + - avoid double - in versionsuffix of torchtext easyconfig (#10472) + - fix Mako easyconfigs using a */2018* toolchain (#10480) + - move builddependencies to dependencies in OTF2 and Score-P easyconfigs(#10496) + - add patch for UCX 1.8.0 to fix unresolved symbol (#10499) + - add missing cURL dep for LAMMPS (#10527) + - fix R 3.6.3 on Power9 (#10531) + - add Python 2 builddep for OpenPGM (#10539) + - add ibverbs dependencies via constants to PyTorch 1.4.0 easyconfigs (#10540) + - add missing Bison build dep in Graphviz easyconfigs (#10541) + - use https in homepage for Mathematica 12.0.0 + clean up sanity check commands (now done by easyblock) (#10559) + - add missing PyVCF dependency for BAMSurgeon (#10564) + - remove FFTW dependencies from LAMMPS easyconfigs, no longer needed (MKL can be used too now) (#10565) + - fix building [foss/2019b] ITK v5.0.1 (locale & libjpeg) (#10592) + - fix missing const qualifiers for ncurses (#10606) + - fix OS dependency for rstudio for Debian-based systems (#10608) + - fix Rmath paths in FastQTL/2.184 (#10612) + - add symlink for Arlequin commands + fix sanity check commands (#10620) + - add patch for h5py 2.10.0 with 2020a toolchains to avoid MPI_Init at import (#10626) + - fix Mako easyconfigs using a 2016 & 2017 toolchain (#10627) + - fix binutils for Fedora 32 / GCC 10 (#10633) + - stop using old hpcugent URL for cloning framework/easyblocks repos in CI (#10635) + - replace /path/to with actual installation prefix in FuSeq scripts (#10640) +- other changes: + - use Bison 3.3.2 as build dep for flex 2.6.4 (#10403) + - remove patch leftovers from AutoMap v1.0 (#10419) + - mention http:// Pfam website rather than ftp:// in load message of BiG-SCAPE easyconfig (#10439) + - archive old Singularity configs (#10591) + - don't use harmful patch for h5py 2.10.0 with foss/2020a + pull out h5py 2.10.0 easyconfig using intel/2020a (#10630) + - use SYSTEM constant for toolchain in easyconfigs already use 'system' toolchain (#10638) + + v4.2.0 (April 14th 2020) ------------------------ From d854bac04ef531c10163054b49a51d9efbf7f87f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 May 2020 14:02:04 +0800 Subject: [PATCH 430/431] update version to 4.2.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f0a4f882e5a..c214435cbf6 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.2.1.dev0' +VERSION = '4.2.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From a95387b753ecf93b152e2a6daa2ee8928c6b2967 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2020 10:08:58 +0200 Subject: [PATCH 431/431] minor tweaks to EasyBuild v4.2.1 release notes --- RELEASE_NOTES | 96 +++++++++++++++++++++++++-------------------------- 1 file changed, 48 insertions(+), 48 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 14d6f493b71..4b27e444830 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 9,898 easyconfig files, for 1,978 different software packages, +The latest version of easybuild-easyconfig provides 9,894 easyconfig files, for 1,978 different software packages, incl. 31 different (compiler) toolchains. v4.2.1 (May 20th 2020) @@ -11,77 +11,77 @@ v4.2.1 (May 20th 2020) update/bugfix release +- added easyconfigs for new common toolchains: foss/2020a (#10483, #10492), intel/2020a (#10494) - added example easyconfig files for 66 new software packages: - - Alpha (#9994), Arlequin (#10620), AutoMap (#10419), antiSMASH (#10589), artic-ncov2019 (#10459), augur (#10405), - Bio-EUtilities (#10037), CaSpER (#10593), CoCoALib (#10429), cdbfasta (#10547), cddlib (#10429), - DoubletFinder (#10603), dftd3-lib (#10351), E-ANTIC (#10429), FIX (#8870), FastViromeExplorer (#10571), - FusionCatcher (#10134), geopandas (#10322), goalign (#10469), gotree (#10459), gretl (#10413), HDF-EOS (#10534), - HDF-EOS5 (#10536), HMMER2 (#10588), HyPo (#10642), harmony (#10604), king (#10365), libdeflate (#10459), - libfabric (#10616), libgit2 (#10453), libuv (#10444), MDAnalysis (#10545), MEM (#10605), MESS (#10597), - MinCED (#10037), MitoZ (#7735), mbuffer (#10524), metaerg (#10037), NLMpy (#10029), NTL (#10431), nauty (#10429), - nifti2dicom (#10598), ntCard (#10502), ProtHint (#10549), PyVCF (#10564), PyWavelets (#10501), pIRS (#10508), - popscle (#10550), protozero (#10495), pysndfx (#10452), RNA-Bloom (#10502), rampart (#10459), rickflow (#10641), - root_numpy (#10424), rstudio (#10619), SDSL (#10642), SHAP (#10379), SNPomatic (#10524), ScaFaCoS (#10537), - Scythe (#10524), SoX (#10452), swissknife (#10037),) TCLAP (#10598), Taiyaki (#10573), torchaudio (#10516), - wtdbg2 (#10524) + - Alpha (#9994), antiSMASH (#10589), Arlequin (#10620), artic-ncov2019 (#10459), augur (#10405), AutoMap (#10419), + Bio-EUtilities (#10037), CaSpER (#10593), cdbfasta (#10547), cddlib (#10429), CoCoALib (#10429) + dftd3-lib (#10351), DoubletFinder (#10603), E-ANTIC (#10429), FastViromeExplorer (#10571), FIX (#8870), + FusionCatcher (#10134), geopandas (#10322), goalign (#10469), gotree (#10459), gretl (#10413), harmony (#10604), + HDF-EOS (#10534), HDF-EOS5 (#10536), HMMER2 (#10588), HyPo (#10642), king (#10365), libdeflate (#10459), + libfabric (#10616), libgit2 (#10453), libuv (#10444), mbuffer (#10524), MDAnalysis (#10545), MEM (#10605), + MESS (#10597), metaerg (#10037), MinCED (#10037), MitoZ (#7735), nauty (#10429), nifti2dicom (#10598), + NLMpy (#10029), ntCard (#10502), NTL (#10431), pIRS (#10508), popscle (#10550), ProtHint (#10549), + protozero (#10495), pysndfx (#10452), PyVCF (#10564), PyWavelets (#10501), rampart (#10459), rickflow (#10641), + RNA-Bloom (#10502), root_numpy (#10424), rstudio (#10619), ScaFaCoS (#10537), Scythe (#10524), SDSL (#10642), + SHAP (#10379), SNPomatic (#10524), SoX (#10452), swissknife (#10037),) Taiyaki (#10573), TCLAP (#10598), + torchaudio (#10516), wtdbg2 (#10524) - added additional easyconfigs for various supported software packages, including: - - 4ti2 1.6.9, ADF 2019.303, ARAGORN 1.2.38, ATK 2.36.0, AUGUSTUS 3.3.3, Alpha 20200430, Anaconda3 2020.02.eb, Arb 2.16.0, Arlequin 3.5.2.2, ArviZ 0.7.0, AutoMap 1.0, Autoconf 2.69, Automake 1.16.1, Autotools 20180311, angsd 0.933, angsd 0.933, antiSMASH 5.1.2, archspec 0.1.0, artic ncov2019, at spi2, at spi2, attr 2.4.48, augur 7.0.2, BBMap 38.79, BCFtools 1.10.2, BRAKER 2.1.5, BWA 0.7.17, Bazel 2.0.0, Bio EUtilities, Biopython 1.75, Bison 3.6.1, Blosc 1.17.1, Bonito 0.1.4, Boost.Python 1.72.0, Boost.Python 1.72.0, Boost 1.72.0, Boost 1.72.0, Bowtie 1.2.3, Bowtie2 2.4.1, bcl2fastq2 2.20.0, binutils 2.34, bzip2 1.0.8, CITE seq, CLISP 2.49, CMake 3.16.4, CPLEX 12.10, CVXOPT 1.2.4, CaSpER 2.0, CoCoALib 0.99601, Coreutils 8.32, CubeLib 4.4.4, CubeWriter 4.4.3, cURL 7.69.1, cairo 1.16.0, cdbfasta 0.99, cdbfasta 0.99, cdbfasta 0.99, cddlib 0.94i, csvkit 1.0.5, ctffind 4.1.13, DB 18.1.32, DBus 1.13.12, DCMTK 3.6.5, DFTB+ 19.1, DFTB+ 19.1, DoubletFinder 2.0.3, Doxygen 1.8.17, dftd3 lib, double conversion, E ANTIC, ETE 3.1.1, EasyBuild 4.2.0.eb, Eigen 3.3.7, Exonerate 2.4.0, ecCodes 2.17.0, ecCodes 2.17.0, expat 2.2.9, FFTW 3.3.8, FFTW 3.3.8, FFmpeg 4.2.2, FIX 1.06.12, FLASH 1.2.11, FLINT 2.5.2, FSL 6.0.2, FSL 6.0.2, FastViromeExplorer 20180422, FriBidi 1.0.9, FusionCatcher 1.20, file 5.38, flex 2.6.4, fontconfig 2.13.92, foss 2020a.eb, freetype 2.10.1, GATK 4.1.5.0, GCC 10.1.0.eb, GCC 9.3.0.eb, GCCcore 10.1.0.eb, GDAL 3.0.4, GDAL 3.0.4, GDCM 3.0.5, GEOS 3.8.1, GEOS 3.8.1, GLPK 4.65, GLib 2.64.1, GMP 6.2.0, GObject Introspection, GROMACS 2020.1, GSL 2.6, GSL 2.6, GST plugins, GStreamer 1.16.2, GTK+ 3.24.17, Gdk Pixbuf, GeneMark ET, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GitPython 3.1.0, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2, GlobalArrays 5.7.2, Guile 1.8.8, gap 4.11.0, gc 7.6.12, geopandas 0.7.0, gettext 0.20.1, gflags 2.2.2, glew 2.1.0, glew 2.1.0, glog 0.4.0, gmpy2 2.1.0b4, gmsh 4.5.6, gnuplot 5.2.8, goalign 0.3.2.eb, gompi 2020a.eb, gotree 0.4.0.eb, gperf 3.1, gpustat 0.6.0, gradunwarp 1.2.0, gradunwarp 1.2.0, gretl 2020a, gzip 1.10, HDDM 0.7.5, HDF EOS, HDF EOS5, HDF5 1.10.6, HDF5 1.10.6, HMMER2 2.3.2, HPL 2.3, HPL 2.3, HTSlib 1.10.2, HarfBuzz 2.6.4, HyPo 1.0.3, Hypre 2.18.2, Hypre 2.18.2, h5py 2.10.0, harmony 1.0.0, help2man 1.47.15, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1, IPython 7.13.0, IPython 7.13.0, IQ TREE, ImageMagick 7.0.10, iccifort 2020.1.217.eb, iimpi 2020a.eb, imkl 2020.1.217, impi 2019.7.217, intel 2020a.eb, intltool 0.51.0, JasPer 2.0.14, Julia 1.4.1, jbigkit 2.1, KMC 3.1.2rc1, Kraken2 2.0.9, kim api, kim api, king 2.2.4.eb, LAME 3.100, LAMMPS 3Mar2020, LLVM 9.0.1, LMDB 0.9.24, LMfit 1.0.0, LZO 2.10, LZO 2.10, LibTIFF 4.1.0, LittleCMS 2.9, Longshot 0.4.1, Lua 5.3.5, libGLU 9.0.1, libarchive 3.4.2, libcerf 1.13, libcroco 0.6.13, libdeflate 1.5, libdrm 2.4.100, libepoxy 1.5.4, libevent 2.1.11, libfabric 1.10.1, libfabric 1.9.1, libffcall 2.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libgeotiff 1.5.1, libgit2 1.0.0, libglvnd 1.2.0, libjpeg turbo, libmatheval 1.1.11, libpciaccess 0.16, libpng 1.6.37, libreadline 8.0, librsvg 2.48.4, libsigsegv 2.12, libsndfile 1.0.28, libsodium 1.0.18, libtool 2.4.6, libunistring 0.9.10, libunwind 1.3.1, libuv 1.37.0, libxc 4.3.4, libxml2 2.9.10, libyaml 0.2.2, lpsolve 5.5.2.5, lrslib 7.0a, lz4 1.9.2, M4 1.4.18, MAFFT 7.427, MDAnalysis 0.20.1, MDAnalysis 0.20.1, MDTraj 1.9.3, MEM 20191023, MEM 20191023, MEME 5.1.1, MEME 5.1.1, MESS 0.1.6, METIS 5.1.0, MPC 1.1.0, MPFR 4.0.2, MUMPS 5.2.1, MUMPS 5.2.1, MUSCLE 3.8.31, Mako 1.1.2, MariaDB connector, Mesa 20.0.2, Meson 0.53.2, MinCED 0.4.2, MinPath 1.4, MitoZ 2.3, MotionCor2 1.3.1, MultiQC 1.8, MultiQC 1.8, Multiwfn 3.6, matplotlib 3.2.1, matplotlib 3.2.1, mbuffer 20191016, metaerg 1.2.3, minimap2 2.17, minimap2 2.17, molmod 1.4.5, molmod 1.4.5, NASM 2.14.02, NCIPLOT 4.0, NGS Python, NGS 2.10.4, NLMpy 0.1.5, NLopt 2.6.1, NSPR 4.25, NSS 3.51, NTL 11.3.4, NWChem 7.0.0, Nextflow 20.04.1.eb, Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, nauty 2.6r12, nauty 2.7rc2, ncbi vdb, ncdf4 1.17, ncurses 6.2, netCDF C++4, netCDF Fortran, netCDF Fortran, netCDF 4.7.4, netCDF 4.7.4, netMHCIIpan 3.2, netcdf4 python, networkx 2.2, networkx 2.4, nifti2dicom 0.4.11, nodejs 12.16.1, ntCard 1.2.1, numactl 2.0.13, numexpr 2.6.5, numexpr 2.7.1, numexpr 2.7.1, OPARI2 2.0.5, OTF2 2.2, OpenBLAS 0.3.9, OpenEXR 2.4.1, OpenMPI 4.0.3, OpenPGM 5.2.122, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PDT 3.25, PETSc 3.12.4, PETSc 3.12.4, PLINK 2.00a2.3_x86_64.eb, PLUMED 2.6.0, PLUMED 2.6.0, PMIx 3.1.5, PROJ 7.0.0, Pango 1.44.7, Perl 5.30.2, Pillow 7.0.0, ProtHint 2.4.0, ProtHint 2.4.0, PyMC3 3.8, PyTables 3.4.4, PyTables 3.6.1, PyTables 3.6.1, PyVCF 0.6.8, PyWavelets 1.1.1, PyYAML 5.3, Python 2.7.18, Python 3.8.2, pIRS 2.0.2, parallel 20200422, patchelf 0.10, pixman 0.38.4, pkg config, pkgconfig 1.5.1, popscle 0.1, protobuf python, protozero 1.6.8, pybind11 2.4.3, pysndfx 0.3.6, python Levenshtein, Qt5 5.14.1, QuantumESPRESSO 6.5, R bundle, R 3.6.3, R 4.0.0, RMBlast 2.9.0, RNA Bloom, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, Rust 1.42.0, Rust 1.42.0, rampart 1.2.0rc3, re2c 1.3, rickflow 0.7.0, rioxarray 0.0.24, root_numpy 4.8.0, rootpy 1.0.1, rstudio 1.2.5033, rstudio 1.2.5042, SAMtools 1.10, SCOTCH 6.0.9, SCOTCH 6.0.9, SCons 3.1.2, SDL2 2.0.10, SDSL 2.1.1, SHAP 0.35.0, SIONlib 1.7.6, SLATEC 4.1, SNPomatic 1.0, SQLite 3.31.1, SRA Toolkit, SRA Toolkit, SWIG 4.0.1, Salmon 1.2.0, ScaFaCoS 1.0.1, ScaFaCoS 1.0.1, ScaLAPACK 2.1.0, SciPy bundle, SciPy bundle, Score P, Scythe 0.994, SeqAn 2.4.0, Singular 4.1.2, SoX 14.4.2, Stacks 2.53, StringTie 2.1.1, SuiteSparse 5.7.1, SuiteSparse 5.7.1, Szip 2.1.1, scikit build, snappy 1.1.8, spaln 2.4.03, swissknife 1.80, sympy 1.5.1, TCLAP 1.2.2, Taiyaki 5.0.1, Taiyaki 5.0.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2, tbb 2020.1, tbl2asn 20200302, torchaudio 0.5.0, torchaudio 0.5.0, torchtext 0.5.0, torchvision 0.5.0, UCX 1.8.0, UDUNITS 2.2.26, UMI tools, utf8proc 2.5.0, util linux, VCFtools 0.1.16, VCFtools 0.1.16, VTK 8.2.0, VTK 8.2.0, Voro++ 0.4.6, worker 1.6.12, wtdbg2 2.5, wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, xorg macros, YAXT 0.6.2, YAXT 0.6.2, Yasm 1.3.0, yaff 1.6.0, ZeroMQ 4.3.2, zlib 1.2.11, zsh 5.8, zstd 1.4.4 -- added easyconfigs for new common toolchains: foss/2020a (#10483), intel/2020a (#10494) + - ADF 2019.303, BRAKER 2.1.5, Bazel 2.0.0, Bonito 0.1.4, Boost.Python 1.72.0, Bowtie2 2.4.1, CMake 3.16.4, + CPLEX 12.10, CVXOPT 1.2.4, Coreutils 8.32, cURL 7.69.1, DFTB+ 19.1, ecCodes 2.17.0, expat 2.2.9, FFmpeg 4.2.2, + FriBidi 1.0.9, GATK 4.1.5.0, GCC(core) 10.1.0, GDAL 3.0.4, GEOS 3.8.1, GLib 2.64.1, GMP 6.2.0, GROMACS 2020.1, + GTK+ 3.24.17, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2, + gmpy2 2.1.0b4, gmsh 4.5.6, gpustat 0.6.0, gradunwarp 1.2.0, HDF5 1.10.6, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1, + IPython 7.13.0, ImageMagick 7.0.10, Julia 1.4.1, KMC 3.1.2rc1, Kraken2 2.0.9, LMfit 1.0.0, Longshot 0.4.1, + libarchive 3.4.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libjpeg-turbo 2.0.4, librsvg 2.48.4, libsigsegv 2.12, + lrslib 7.0a, MEME 5.1.1, MPC 1.1.0, Mako 1.1.2, Mesa 20.0.2, Meson 0.53.2, MotionCor2 1.3.1, MultiQC 1.8, + matplotlib 3.2.1, NGS-Python-2.10.4, NGS 2.10.4, NSPR 4.25, NSS 3.51, NWChem 7.0.0, Nextflow 20.04.1, + Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, ncbi-vdb 2.10.4 netCDF 4.7.4, OpenBLAS 0.3.9, OpenEXR 2.4.1, + OpenMPI 4.0.3, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PLUMED 2.6.0, PMIx 3.1.5, + PROJ 7.0.0, Perl 5.30.2, Pillow 7.0.0, PyYAML 5.3, Python 2.7.18 + 3.8.2, parallel 20200422, Qt5 5.14.1, + R-bundle-Bioconductor 3.11, R 3.6.3 + 4.0.0, RMBlast 2.9.0, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, re2c 1.3, + rioxarray 0.0.24, rootpy 1.0.1, rstudio 1.2.5042, SCons 3.1.2, SDL2 2.0.10, SIONlib 1.7.6, SQLite 3.31.1, + SRA-Toolkit 2.10.4, Salmon 1.2.0, ScaLAPACK 2.1.0, SciPy-bundle 2020.03, Stacks 2.53, StringTie 2.1.1, + SuiteSparse 5.7.1, snappy 1.1.8, spaln 2.4.03, sympy 1.5.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2, + tbl2asn 20200302, torchvision 0.5.0, UCX 1.8.0, UMI-tools 1.0.1, utf8proc 2.5.0, util-linux 2.35, worker 1.6.12, + wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, zsh 5.8, zstd 1.4.4 - minor enhancements, including: - - add mRMRe and dHSIC and sync easyconfig in fosscuda for R v3.6.2 (#10359) - - add Mozilla::CA, Test::RequiresInternet and LWP::Protocol::https extensions to Perl 5.30.x (#10412) - - update extensions in Python 3.8.2 easyconfig (#10456) + - add additional extensions for recent versions of R (#10359, #10585, #10586, #10621) and R-bundle-Bioconductor (#10585, #10596, #10621) + - add additional extensions for recent versions of Perl (#10412, #10546, #10623) - include LLVM linker in Clang 7.0.1 on GCC 7.3.0-2.30(#10458) - include static lib and header in nimimap2 easyconfigs for foss-2018b and GCC-8.2.0* (#10464) - - add UCX 1.8.0 as dep for OpenMPI 4.0.3 using in foss/2020a (+ easyconfig for libfabric 1.9.1) (#10492) - - add MCE::Mutex extension to Perl 5.28.1 + 5.30.x (#10546) - - add additional extensions to R 3.6.2 + R-bundle-Bioconductor 3.10 easyconfigs (#10585) - - add additional extensions to R 3.6.3 & R 4.0.0 extensions (#10586) - - add diffcyt extension to R-bundle-Bioconductor 3.10 (#10596) - add alternate checksum for EMBOSS (#10607) - - update ALL, pRolocdata and geneLenDataBase extensions in Bioconductor/3.11 (#10614) - - add extensions to R 4.0.0 and Bioconductor 3.11 easyconfigs (#10621) - - add additional extensions to Perl-5.30.2 easyconfig (#10623) - various bug fixes, including: - fix incorrect checksums for Amber patches (#8870) - add patches to fix installation of R 3.6.2 on POWER (#9830) - - add system dependencies on ibverbs and remove UCX dependency in libfabric v1.9.1 (#10281) - add missing build dep. pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (#10380) - - check sdist with different python versions (#10388) - - add Perl as a build dependency for Autoconf/Automake on GCCcore/8.3.0(#10408) - - add patch for AutoMap to avoid that it to create a log file in installation directory (#10414) + - add Perl as a build dependency for recent Autoconf/Automake easyconfigs (#10408, #10426) - fix source_urls in ICU easyconfigs (#10417) - disable USER-INTEL package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results (#10418) - fix undefined reference to 'qfloat16::mantissatable' in Qt5-5.13.1-GCCcore-8.3.0 (#10425) - - add Perl build dep for Autoconf/Automake using GCCcore/7.3.0 and GCCcore/8.2.0 toolchains (#10426) - - avoid double - in versionsuffix of torchtext easyconfig (#10472) - - fix Mako easyconfigs using a */2018* toolchain (#10480) - - move builddependencies to dependencies in OTF2 and Score-P easyconfigs(#10496) - - add patch for UCX 1.8.0 to fix unresolved symbol (#10499) + - get rid of double '-' in versionsuffix of torchtext easyconfig (#10472) + - fix broken Mako easyconfigs (#10480, #10627) + - move builddependencies to dependencies in OTF2 and Score-P easyconfigs (#10496) - add missing cURL dep for LAMMPS (#10527) - - fix R 3.6.3 on Power9 (#10531) - - add Python 2 builddep for OpenPGM (#10539) - - add ibverbs dependencies via constants to PyTorch 1.4.0 easyconfigs (#10540) + - add Python 2 build dependency for OpenPGM (#10539) + - use OS_PKG_IBVERBS_DEV constant for OS dependency in PyTorch 1.4.0 easyconfigs (#10540) - add missing Bison build dep in Graphviz easyconfigs (#10541) - use https in homepage for Mathematica 12.0.0 + clean up sanity check commands (now done by easyblock) (#10559) - add missing PyVCF dependency for BAMSurgeon (#10564) - remove FFTW dependencies from LAMMPS easyconfigs, no longer needed (MKL can be used too now) (#10565) - - fix building [foss/2019b] ITK v5.0.1 (locale & libjpeg) (#10592) - - fix missing const qualifiers for ncurses (#10606) + - fix ITK v5.0.1 easyconfig w.r.t. locale and location of libjpeg-turbo library (#10592) + - add patch to fix missing const qualifiers for ncurses (#10606) - fix OS dependency for rstudio for Debian-based systems (#10608) - - fix Rmath paths in FastQTL/2.184 (#10612) + - fix Rmath paths in easyconfig for FastQTL v2.184 (#10612) - add symlink for Arlequin commands + fix sanity check commands (#10620) - - add patch for h5py 2.10.0 with 2020a toolchains to avoid MPI_Init at import (#10626) - - fix Mako easyconfigs using a 2016 & 2017 toolchain (#10627) - - fix binutils for Fedora 32 / GCC 10 (#10633) - - stop using old hpcugent URL for cloning framework/easyblocks repos in CI (#10635) - - replace /path/to with actual installation prefix in FuSeq scripts (#10640) + - fix recent binutils easyconfigs usign system toolchain for Fedora 32 / GCC 10 (#10633) + - replace '/path/to' with actual installation prefix in FuSeq scripts (#10640) - other changes: + - check sdist with different Python versions in CI (#10388) - use Bison 3.3.2 as build dep for flex 2.6.4 (#10403) - - remove patch leftovers from AutoMap v1.0 (#10419) - mention http:// Pfam website rather than ftp:// in load message of BiG-SCAPE easyconfig (#10439) - archive old Singularity configs (#10591) - - don't use harmful patch for h5py 2.10.0 with foss/2020a + pull out h5py 2.10.0 easyconfig using intel/2020a (#10630) + - Singularity is not well suited to install via EasyBuild because it requires admin privileges to enable setuid + - stop using old hpcugent URL for cloning framework/easyblocks repos in CI (#10635) - use SYSTEM constant for toolchain in easyconfigs already use 'system' toolchain (#10638)