Merge pull request #9690 from easybuilders/4.1.x

release EasyBuild v4.1.1
easybuilders · Jan 16, 2020 · 9a94292 · 9a94292
2 parents 5ee24bb + 1063f16
commit 9a94292
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diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -30,7 +30,10 @@ jobs:
 
     - name: install OS & Python packages
       run: |
-        sudo apt-get update
+        # apt-get update is disabled for now, because it was failing in GitHub since Fri Dec 13th 2019,
+        # due to 'Conflicting distribution' issue
+        # sudo apt-get update
+        #
         # for modules tool
         sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
         # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -3,9 +3,76 @@ 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 8,748 easyconfig files, for 1,771 different software packages,
+The latest version of easybuild-easyconfig provides 8,964 easyconfig files, for 1,798 different software packages,
 incl. 31 different (compiler) toolchains.
 
+v4.1.1 (January 16th 2020)
+--------------------------
+
+update/bugfix release
+
+- added example easyconfig files for 27 new software packages:
+  - Autoconf-archive (#9658), breseq (#9603), CrossMap (#9483), CSBDeep (#9560), CNT-ILP (#9323), cytoolz (#9453), Faber (#9553),
+    Fiji (#8748), GARLI (#9404), Globus-CLI (#9565), GtkSourceView (#9526), gradunwarp (#9648), gsettings-desktop-schemas (#9529),
+    HyPhy (#9405), horton (#7449), IGMPlot (#9438), LEMON (#9323), Meld (#9530), mhcflurry (#9554), NCIPLOT (#9419), ncl (#9632),
+    OpenSlide (#9499), openslide-python (#9499), pythran (#9488, #9594), Qualimap (#9411), TinyDB (#9555), TreeShrink (#9381)
+- added additional easyconfigs for various supported software packages, including:
+  - Beast 1.10.4, Boost.Python 1.71.0, Clang 9.0.1, ESMF 8.0.0, FSL 6.0.3, fastp 0.20.0, freeglut 3.2.1, GDAL 3.0.2,
+    GEOS 3.8.0, GROMACS 2019.4, GSL 2.6, hwloc 2.1.0, Jellyfish 2.3.0, Julia 1.3.1, LibTIFF 4.1.0, libxml2 2.9.10,
+    lxml 4.4.2, Mothur 1.43.0, mayavi 4.7.1, molmod 1.4.5, netCDF-C++4 4.3.1, netCDF-Fortran 4.5.2, numactl 2.0.13,
+    OpenFOAM 7, OpenFOAM v1912, OpenMM 7.4.1, OpenMPI 4.0.2, PLUMED 2.5.3, PROJ 6.2.1, plotly.py 4.4.1,
+    pocl 1.4, QuickFF 2.2.4, R 3.6.2 w/ foss/2019b and fosscuda/2019b, ReFrame 2.20, SAMtools 1.10, SUNDIALS 5.1.0,
+    SWIG 4.0.1, Salmon 1.0.0, SuiteSparse 5.6.0, snakemake 5.7.1, TensorFlow 2.1.0 w/ fosscuda/2019b, torchvision 0.4.2,
+    WPS 4.1, WRF 4.1.3
+- added easyconfigs for intel/2020.00 toolchain (#9575)
+- minor enhancements, including:
+  - add POWER9 support to CUDA 10.1 easyconfigs (#9442)
+  - build CMake in parallel (#9543)
+  - use NCCL for GPU ops in Horovod 0.18.2 easyconfig (#9562)
+  - update Java/1.8 wrapper to Java/1.8.0_231 (for x86_64) (#9585)
+- various bug fixes, including:
+  - fix remote launch of broker and workers for SCOOP (#9366)
+  - fix failing RPATH sanity check for NCL 6.6.2 due to missing dependencies (+ add easyconfig using foss/2018b) (#9388)
+  - add missing 'wheel' extensions to Spark 2.4.0 easyconfig using intel/2018b toolchain (#9424)
+  - add missing OS dependencies in Java 1.8 easyconfig used on POWER systems (#9454)
+  - fix build of recent Bazel versions on Power9 + stick to Java/1.8 as dependency (#9455)
+  - fix CMake 3.15.3 build on Power (+ enable building in parallel) (#9469)
+  - fix source URLs in xorg-macros easyconfigs (#9477, #9578)
+  - add missing wcwidth extension to Python 2.7.15 + 2.7.16 easyconfigs & enable 'pip check' in sanity check (#9479)
+  - remove (wrong) GI_TYPELIB_PATH and XDG_DATA_DIRS in various easyconfigs (#9528, #9577, #9615)
+  - use xorg-macros as dependency in X11 easyconfigs (rather than installing it as a bundle component) (#9546)
+  - fix lpsymphony extension for R-bundle-Bioconductor (#9548)
+  - add correct 'old-versions' source URL to all Mesa easyconfigs (#9569)
+  - add missing SHA256 checksums for Armadillo (#9572)
+  - also define $AUGUSTUS_BIN_PATH and $AUGUSTUS_SCRIPTS_PATH in generated module file for AUGUSTUS (#9579)
+  - add SSL OS dependencies for GDAL 3.0.0 (#9586)
+  - add missing jupyter_contrib_core extension for IPython 7.7.0+ + consistently include jupyter_nbextensions_configurator extension (#9587)
+  - patch libcxx (Clang 8.0.0) on pcc64le for incomplete IBM128 long double in GCC (#9590)
+  - patch for GCCcore 8.2.0 to fix '__float128 is not supported on this target' on ppc64le (#9591)
+  - fix broken easyconfigs for cyvcf2 v0.11.5 by adding missing 'monotonic' extension (#9601)
+  - use absolute path for extraction to allow relocating the build dir for g2log-1.0 (#9604)
+  - add alternate SHA256 checksum for kallisto-0.43.1 after re-release under same version without code changes (#9611)
+  - add additional valid checksum for MASS 7.3-51.4 extension in R 3.6.0 easyconfigs (#9621)
+  - update ctffind website (#9622)
+  - make sure we use easybuild Clang in pocl easyconfigs (#9624)
+  - make postinstallcmds independent of current working directory in OpenCV 3.1.0 easyconfigs (#9628)
+  - update source_urls to include old releases folder in libsodium easyconfigs (#9632)
+  - fix source URLs for ant v1.10.5 - v1.10.7 (#9633)
+  - update URLs to new location of libxc (#9635)
+  - add alternate SHA256 checksum for rda_1.0.2-2.1 extension in R 3.6.0 (#9644)
+  - update source URLs in QCA 2.1.0 easyconfigs (#9647)
+  - fix Python 3.5.1 easyconfig: bitstring 3.1.3 sources no longer available on PyPI) (#9649)
+  - fix tesseract 4.1.0 dependencies (#9650)
+  - make ICU 64.2 depend on Python3 instead of Python 2, to avoid picking up system Python 3.x (#9652)
+  - use True (boolean value) rather than 'True' (string value) for boolean easyconfig parameters (#9657)
+  - fix pyfits easyconfig by adding missing d2to1 extension (#9687)
+- other changes:
+  - disable running of 'sudo apt-get update' in GitHub CI config, since it's failing (and we don't really need it) (#9492)
+  - require that sanity_pip_check is enabled in new/changed easyconfigs (#9516, #9576)
+  - update copyright statements for 2020 (#9598)
+  - allow missing '-Python-*' versionsuffix for existing easyconfig files changed in PRs (#9634)
+
+
 v4.1.0 (December 4th 2019)
 --------------------------
 

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.18.0-intel-2016a.eb
@@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'}
 
 source_urls = [FTPGNOME_SOURCE]
 sources = [SOURCELOWER_TAR_XZ]
+checksums = ['ce6c48d77bf951083029d5a396dd552d836fff3c1715d3a7022e917e46d0c92b']
 
 local_glibver = '2.47.5'
 dependencies = [
@@ -23,10 +24,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-foss-2016a.eb
@@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2016a'}
 
 source_urls = [FTPGNOME_SOURCE]
 sources = [SOURCELOWER_TAR_XZ]
+checksums = ['493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0']
 
 dependencies = [
     ('GLib', '2.48.0'),
@@ -22,10 +23,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.20.0-intel-2016a.eb
@@ -14,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2016a'}
 
 source_urls = [FTPGNOME_SOURCE]
 sources = [SOURCELOWER_TAR_XZ]
+checksums = ['493a50f6c4a025f588d380a551ec277e070b28a82e63ef8e3c06b3ee7c1238f0']
 
 dependencies = [
     ('GLib', '2.48.0'),
@@ -22,10 +23,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-foss-2016b.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.22.0-intel-2016b.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.0-intel-2017a.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-foss-2018b.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-foss-2017b.eb
@@ -25,10 +25,6 @@ dependencies = [('GLib', '2.53.5')]
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.27.1-intel-2017b.eb
@@ -25,10 +25,6 @@ dependencies = [('GLib', '2.53.5')]
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018a.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-foss-2018b.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb
@@ -28,10 +28,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-intel-2018a.eb
@@ -27,10 +27,6 @@ dependencies = [
 
 configopts = "--enable-introspection=yes"
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb
@@ -31,10 +31,6 @@ dependencies = [
 configopts = "--buildtype=release --default-library=both "
 configopts += "-Dintrospection=true "
 
-modextrapaths = {
-    'XDG_DATA_DIRS': 'share',
-}
-
 sanity_check_paths = {
     'files': ['lib/libatk-1.0.%s' % SHLIB_EXT],
     'dirs': [],

diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb
@@ -15,6 +15,10 @@ source_urls = [
 ]
 sources = [SOURCELOWER_TAR_GZ]
 patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch']
+checksums = [
+    'a1af128aefd228dea0c46d6f5234910fdf068a2b9133175ca8da3af639cb4514',  # augustus-3.2.3.tar.gz
+    '12870afdd184c11d49268ddb9ec2bf81dc3ccce74072857990a7aac07d8b4d7d',  # AUGUSTUS-3.2.3_fix-hardcoding.patch
+]
 
 dependencies = [
     ('zlib', '1.2.11'),
@@ -40,6 +44,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+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/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb
@@ -8,7 +8,10 @@ description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic s
 
 toolchain = {'name': 'foss', 'version': '2018a'}
 
-source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/']
+source_urls = [
+    'http://bioinf.uni-greifswald.de/augustus/binaries/',
+    'http://bioinf.uni-greifswald.de/augustus/binaries/old/',
+]
 sources = ['augustus-%(version)s.tar.gz']
 patches = [
     '%(name)s-%(version)s_bamtools_includepath.patch',
@@ -44,6 +47,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+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/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb
@@ -9,7 +9,10 @@ description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic s
 
 toolchain = {'name': 'foss', 'version': '2017b'}
 
-source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/']
+source_urls = [
+    'http://bioinf.uni-greifswald.de/augustus/binaries/',
+    'http://bioinf.uni-greifswald.de/augustus/binaries/old/',
+]
 sources = ['augustus-%(version)s.tar.gz']
 patches = [
     '%(name)s-%(version)s_fix-hardcoding.patch',
@@ -50,6 +53,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+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/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb
@@ -46,6 +46,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+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/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb
@@ -53,6 +53,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+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/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb
@@ -54,6 +54,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+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/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb
@@ -51,6 +51,10 @@ sanity_check_paths = {
 }
 
 modextrapaths = {'PATH': 'scripts'}
-modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'}
+modextravars = {
+    'AUGUSTUS_BIN_PATH': '%(installdir)s/bin',
+    'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config',
+    'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts',
+}
 
 moduleclass = 'bio'