-
Notifications
You must be signed in to change notification settings - Fork 702
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #17985 from easybuilders/4.7.x
release EasyBuild v4.7.2
- Loading branch information
Showing
606 changed files
with
25,338 additions
and
150 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| ## | ||
| # This is a contribution from SIB Swiss Institute of Bioinformatics | ||
| # Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it | ||
| # | ||
| # Authors:: Sebastien Moretti <[email protected]> | ||
| # | ||
| ## | ||
|
|
||
| # JAR files are in a subdirectory with other stuff, so use Binary | ||
| easyblock = 'Binary' | ||
|
|
||
| name = 'AGeNT' | ||
| version = '3.0.6' | ||
|
|
||
| homepage = 'https://www.agilent.com/en/product/next-generation-sequencing/' | ||
| homepage += 'hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879' | ||
| description = """The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software | ||
| module that processes the read sequences from targeted high-throughput sequencing data | ||
| generated by sequencing Agilent SureSelect and HaloPlex libraries. | ||
| The Trimmer utility of the AGeNT module processes the read sequences to identify and | ||
| remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). | ||
| The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information | ||
| from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with | ||
| options to either mark or merge duplicate reads and output in BAM file format. The Illumina | ||
| InterOp libraries are a set of common routines used for reading InterOp metric files | ||
| produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards | ||
| compatible and capable of supporting prior releases of the software, with one exception: | ||
| GA systems have been excluded.""" | ||
|
|
||
| software_license = 'LicenseVeryRestrictive' | ||
| # For Research Use Only. Not for use in diagnostic procedures. | ||
|
|
||
| toolchain = SYSTEM | ||
|
|
||
| builddependencies = [ | ||
| ('UnZip', '6.0', '', ('GCCcore', '10.3.0')), | ||
| ] | ||
| dependencies = [ | ||
| ('Java', '11'), | ||
| ] | ||
|
|
||
| # Fill the form at https://explore.agilent.com/AGeNT-Software-Download-Form | ||
| # to get the zip file. | ||
| sources = ['AGeNT_%(version)s.zip'] | ||
| checksums = ['746e4445567ee41b7ced5cab3cd252d27d8f6f9eab56766e5d7ca74894e3db73'] | ||
|
|
||
| extract_sources = False | ||
|
|
||
| install_cmd = 'unzip ' + sources[0] + ' && ' | ||
| install_cmd += 'cp -ar *.html *.md agent/* %(installdir)s/ && ' | ||
| install_cmd += 'chmod -x %(installdir)s/*.txt && ' | ||
| install_cmd += 'chmod -x %(installdir)s/*.md && ' | ||
| install_cmd += 'rm -f %(installdir)s/*.cmd && ' | ||
| install_cmd += 'rm -f %(installdir)s/*.html && ' | ||
| install_cmd += 'mkdir %(installdir)s/bin && ' | ||
| install_cmd += 'mv %(installdir)s/*.sh %(installdir)s/bin/ && ' | ||
| install_cmd += 'ln -s ../lib %(installdir)s/bin/lib && ' | ||
| install_cmd += 'sed -i "s@ lib/@ ../lib/@" %(installdir)s/bin/*.sh' | ||
|
|
||
| sanity_check_paths = { | ||
| 'files': ['bin/agent.sh'], | ||
| 'dirs': ['bin', 'lib'] | ||
| } | ||
|
|
||
| sanity_check_commands = ["agent.sh"] | ||
|
|
||
| moduleclass = 'bio' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| easyblock = 'PythonBundle' | ||
|
|
||
| name = 'ASE' | ||
| version = '3.22.1' | ||
|
|
||
| homepage = 'https://wiki.fysik.dtu.dk/ase' | ||
| description = """ASE is a python package providing an open source Atomic Simulation Environment | ||
| in the Python scripting language. | ||
| From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations | ||
| in C of functions in ASE. ASE uses it automatically when installed.""" | ||
|
|
||
| toolchain = {'name': 'gfbf', 'version': '2022b'} | ||
|
|
||
| dependencies = [ | ||
| ('Python', '3.10.8'), | ||
| ('SciPy-bundle', '2023.02'), | ||
| ('Flask', '2.2.3'), | ||
| ('matplotlib', '3.7.0'), | ||
| ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE | ||
| ('spglib-python', '2.0.2'), # optional | ||
| ] | ||
|
|
||
| use_pip = True | ||
| sanity_pip_check = True | ||
|
|
||
| exts_list = [ | ||
| ('pytest-mock', '3.8.2', { | ||
| 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], | ||
| }), | ||
| ('ase', version, { | ||
| 'patches': [ | ||
| 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', | ||
| 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', | ||
| 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', | ||
| 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', | ||
| ], | ||
| 'checksums': [ | ||
| '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz | ||
| # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch | ||
| '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', | ||
| # ASE-3.22.1-Compatibility-with-pytest-part-2.patch | ||
| '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', | ||
| # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch | ||
| 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', | ||
| # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch | ||
| '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', | ||
| ], | ||
| }), | ||
| ('ase-ext', '20.9.0', { | ||
| 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], | ||
| }), | ||
| ] | ||
|
|
||
| sanity_check_paths = { | ||
| 'files': ['bin/ase'], | ||
| 'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
| } | ||
|
|
||
| # make sure Tkinter is available, otherwise 'ase gui' will not work | ||
| sanity_check_commands = ["python -c 'import tkinter' "] | ||
|
|
||
| moduleclass = 'chem' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| easyblock = 'PythonBundle' | ||
|
|
||
| name = 'ASE' | ||
| version = '3.22.1' | ||
|
|
||
| homepage = 'https://wiki.fysik.dtu.dk/ase' | ||
| description = """ASE is a python package providing an open source Atomic Simulation Environment | ||
| in the Python scripting language. | ||
| From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations | ||
| in C of functions in ASE. ASE uses it automatically when installed.""" | ||
|
|
||
| toolchain = {'name': 'gomkl', 'version': '2021a'} | ||
|
|
||
| dependencies = [ | ||
| ('Python', '3.9.5'), | ||
| ('SciPy-bundle', '2021.05'), | ||
| ('Flask', '1.1.4'), | ||
| ('matplotlib', '3.4.2'), | ||
| ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE | ||
| ('spglib-python', '1.16.1'), # optional | ||
| ] | ||
|
|
||
| use_pip = True | ||
| sanity_pip_check = True | ||
|
|
||
| exts_list = [ | ||
| ('pytest-mock', '3.6.1', { | ||
| 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], | ||
| }), | ||
| ('ase', version, { | ||
| 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], | ||
| }), | ||
| ('ase-ext', '20.9.0', { | ||
| 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], | ||
| }), | ||
| ] | ||
|
|
||
| sanity_check_paths = { | ||
| 'files': ['bin/ase'], | ||
| 'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
| } | ||
|
|
||
| # make sure Tkinter is available, otherwise 'ase gui' will not work | ||
| sanity_check_commands = ["python -c 'import tkinter' "] | ||
|
|
||
| moduleclass = 'chem' |
31 changes: 31 additions & 0 deletions
31
easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| easyblock = 'CMakeMake' | ||
|
|
||
| name = 'Abseil' | ||
| version = '20230125.2' | ||
|
|
||
| homepage = 'https://abseil.io/' | ||
| description = """Abseil is an open-source collection of C++ library code designed to augment the | ||
| C++ standard library. The Abseil library code is collected from Google's own | ||
| C++ code base, has been extensively tested and used in production, and is the | ||
| same code we depend on in our daily coding lives.""" | ||
|
|
||
| toolchain = {'name': 'GCCcore', 'version': '12.2.0'} | ||
| toolchainopts = {'pic': True, 'cstd': 'c++17'} | ||
|
|
||
| source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] | ||
| sources = ['%(version)s.tar.gz'] | ||
| checksums = ['9a2b5752d7bfade0bdeee2701de17c9480620f8b237e1964c1b9967c75374906'] | ||
|
|
||
| builddependencies = [ | ||
| ('binutils', '2.39'), | ||
| ('CMake', '3.24.3'), | ||
| ] | ||
|
|
||
| configopts = '-DBUILD_SHARED_LIBS=ON ' | ||
|
|
||
| sanity_check_paths = { | ||
| 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], | ||
| 'dirs': ['include/absl'], | ||
| } | ||
|
|
||
| moduleclass = 'lib' |
31 changes: 31 additions & 0 deletions
31
easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| easyblock = 'CMakeMake' | ||
|
|
||
| name = 'Abseil' | ||
| version = '20230125.3' | ||
|
|
||
| homepage = 'https://abseil.io/' | ||
| description = """Abseil is an open-source collection of C++ library code designed to augment the | ||
| C++ standard library. The Abseil library code is collected from Google's own | ||
| C++ code base, has been extensively tested and used in production, and is the | ||
| same code we depend on in our daily coding lives.""" | ||
|
|
||
| toolchain = {'name': 'GCCcore', 'version': '12.3.0'} | ||
| toolchainopts = {'pic': True, 'cstd': 'c++17'} | ||
|
|
||
| source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] | ||
| sources = ['%(version)s.tar.gz'] | ||
| checksums = ['5366d7e7fa7ba0d915014d387b66d0d002c03236448e1ba9ef98122c13b35c36'] | ||
|
|
||
| builddependencies = [ | ||
| ('binutils', '2.40'), | ||
| ('CMake', '3.26.3'), | ||
| ] | ||
|
|
||
| configopts = '-DBUILD_SHARED_LIBS=ON ' | ||
|
|
||
| sanity_check_paths = { | ||
| 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], | ||
| 'dirs': ['include/absl'], | ||
| } | ||
|
|
||
| moduleclass = 'lib' |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.