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Merge pull request #21410 from easybuilders/4.9.x
release EasyBuild v4.9.3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| # easybuild easyconfig | ||
| # | ||
| # John Dey <[email protected]> Fred Hutchinson Cancer Center | ||
| # Thomas Eylenbosch - Gluo NV | ||
| # Update: Petr Král (INUITS) | ||
| # | ||
| easyblock = 'Bundle' | ||
|
|
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| name = 'AGAT' | ||
| version = '1.4.0' | ||
|
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| homepage = 'https://agat.readthedocs.io/en/latest/' | ||
| description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations | ||
| in any GTF/GFF format.""" | ||
|
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| toolchain = {'name': 'GCC', 'version': '12.3.0'} | ||
|
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| builddependencies = [('binutils', '2.40')] | ||
|
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| dependencies = [ | ||
| ('Perl', '5.36.1'), | ||
| ('BioPerl', '1.7.8'), | ||
| ] | ||
|
|
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| exts_defaultclass = 'PerlModule' | ||
| exts_filter = ("perl -e 'require %(ext_name)s'", '') | ||
|
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| exts_list = [ | ||
| ('Set::Object', '1.42', { | ||
| 'source_tmpl': 'Set-Object-%(version)s.tar.gz', | ||
| 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], | ||
| 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], | ||
| }), | ||
| ('File::Share', '0.27', { | ||
| 'source_tmpl': 'File-Share-%(version)s.tar.gz', | ||
| 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], | ||
| 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], | ||
| }), | ||
| ('Sort::Naturally', '1.03', { | ||
| 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', | ||
| 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], | ||
| 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], | ||
| }), | ||
| ('Class::MethodMaker', '2.24', { | ||
| 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', | ||
| 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], | ||
| 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], | ||
| }), | ||
| ('Term::ProgressBar', '2.23', { | ||
| 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', | ||
| 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], | ||
| 'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'], | ||
| }), | ||
| (name, version, { | ||
| 'modulename': 'AGAT::Utilities', | ||
| 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], | ||
| 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], | ||
| 'checksums': ['d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77'], | ||
| }), | ||
| ] | ||
|
|
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| modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} | ||
|
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| sanity_check_paths = { | ||
| 'files': [], | ||
| 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], | ||
| } | ||
|
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| sanity_check_commands = ['agat_convert_bed2gff.pl --help'] | ||
| moduleclass = 'bio' |
36 changes: 36 additions & 0 deletions
36
easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-12.3.0-Java-11.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| easyblock = 'ConfigureMake' | ||
|
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| name = 'ANTLR' | ||
| version = '2.7.7' | ||
| versionsuffix = '-Java-%(javaver)s' | ||
|
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| homepage = 'https://www.antlr2.org/' | ||
| description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) | ||
| is a language tool that provides a framework for constructing recognizers, | ||
| compilers, and translators from grammatical descriptions containing | ||
| Java, C#, C++, or Python actions.""" | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '12.3.0'} | ||
|
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| source_urls = ['https://www.antlr2.org/download/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| patches = ['%(name)s-%(version)s_includes.patch'] | ||
| checksums = [ | ||
| '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz | ||
| 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch | ||
| ] | ||
|
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| builddependencies = [('binutils', '2.40')] | ||
|
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| dependencies = [('Java', '11', '', SYSTEM)] | ||
|
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| configopts = '--disable-examples --disable-csharp --disable-python' | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/antlr', 'bin/antlr-config'], | ||
| 'dirs': ['include'], | ||
| } | ||
|
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| sanity_check_commands = ["antlr --help"] | ||
|
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| moduleclass = 'tools' |
51 changes: 51 additions & 0 deletions
51
easybuild/easyconfigs/a/APOST3D/APOST3D-20240527-intel-compilers-2023.1.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| easyblock = 'CmdCp' | ||
|
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| name = 'APOST3D' | ||
| version = '20240527' | ||
| local_commit = 'e06c8b0' | ||
|
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| description = """ | ||
| Open-source APOST-3D software features a large number of wavefunction analysis tools developed | ||
| over the past 20 years, aiming at connecting classical chemical concepts with the electronic | ||
| structure of molecules. APOST-3D relies on the identification of the atom in the molecule | ||
| (AIM), and several analysis tools are implemented in the most general way so that they can be | ||
| used in combination with any chosen AIM. | ||
| A Fortran-based code developed at the Universitat de Girona (UdG) by P. Salvador and collaborators. | ||
| """ | ||
| homepage = 'https://github.com/mgimferrer/APOST3D' | ||
|
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| toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} | ||
|
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| builddependencies = [ | ||
| ('make', '4.4.1'), | ||
| ] | ||
|
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| source_urls = ['https://github.com/mgimferrer/APOST3D/archive'] | ||
| sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] | ||
| checksums = ['1eb9a0f97b4dd135b782b96cadc37b3acfc27c69521cf3aab6cc10d4fc9292af'] | ||
|
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| local_cmds = ' export APOST3D_PATH=%(start_dir)s && ' | ||
| # Compile provided Libxc version 4.2.3 | ||
| # (it is not possible to couple APOST-3D with newer Libxc libraries): | ||
| local_cmds += 'bash compile_libxc.sh && ' | ||
| # Compile | ||
| local_cmds += 'make -f Makefile_profgen && ' | ||
| # Run test calculations on single-processor: | ||
| local_cmds += 'bash compiler-runtest && ' | ||
| # Recompile using info geneated in previous step | ||
| local_cmds += 'make -f Makefile_profuse && ' | ||
| # Run test calculations in parallel: | ||
| local_cmds += 'bash compiler-runtest2' | ||
|
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| cmds_map = [('.*', local_cmds)] | ||
|
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| local_bin_files = ['apost3d', 'apost3d-eos', 'eos_aom'] | ||
|
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| files_to_copy = [(local_bin_files, 'bin')] | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % f for f in local_bin_files], | ||
| 'dirs': [''], | ||
| } | ||
|
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| moduleclass = 'chem' |
32 changes: 32 additions & 0 deletions
32
easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-13.3.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| easyblock = 'ConfigureMake' | ||
|
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| name = 'APR-util' | ||
| version = '1.6.3' | ||
|
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| homepage = 'https://apr.apache.org/' | ||
| description = "Apache Portable Runtime (APR) util libraries." | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '13.3.0'} | ||
|
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| source_urls = ['https://archive.apache.org/dist/apr/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983'] | ||
|
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| builddependencies = [('binutils', '2.42')] | ||
|
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| dependencies = [ | ||
| ('APR', '1.7.4'), | ||
| ('SQLite', '3.45.3'), | ||
| ('expat', '2.6.2'), | ||
| ] | ||
|
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| configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " | ||
|
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| sanity_check_paths = { | ||
| 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], | ||
| 'dirs': ["include/apr-1"], | ||
| } | ||
|
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| parallel = 1 | ||
|
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| moduleclass = 'tools' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| easyblock = 'ConfigureMake' | ||
|
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| name = 'APR' | ||
| version = '1.7.4' | ||
|
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| homepage = 'https://apr.apache.org/' | ||
| description = "Apache Portable Runtime (APR) libraries." | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '13.3.0'} | ||
|
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| source_urls = ['https://archive.apache.org/dist/apr/'] | ||
| sources = [SOURCELOWER_TAR_GZ] | ||
| checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9'] | ||
|
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| builddependencies = [('binutils', '2.42')] | ||
|
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| sanity_check_paths = { | ||
| 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], | ||
| 'dirs': ["include/apr-1"], | ||
| } | ||
|
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| moduleclass = 'tools' |
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