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Merge pull request #21463 from easybuilders/4.9.x
release EasyBuild v4.9.4
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| easyblock = 'MesonNinja' | ||
|
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| name = 'ATK' | ||
| version = '2.38.0' | ||
|
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| 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. | ||
| """ | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '13.3.0'} | ||
|
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| source_urls = [FTPGNOME_SOURCE] | ||
| sources = [SOURCELOWER_TAR_XZ] | ||
| checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] | ||
|
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| builddependencies = [ | ||
| ('binutils', '2.42'), | ||
| ('Meson', '1.4.0'), | ||
| ('Ninja', '1.12.1'), | ||
| ('pkgconf', '2.2.0'), | ||
| ('GObject-Introspection', '1.80.1'), | ||
| ] | ||
|
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| dependencies = [ | ||
| ('GLib', '2.80.4'), | ||
| ] | ||
|
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| configopts = "--buildtype=release --default-library=both " | ||
| configopts += "-Dintrospection=true " | ||
|
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| sanity_check_paths = { | ||
| 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], | ||
| 'dirs': [], | ||
| } | ||
|
|
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| moduleclass = 'vis' |
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73 changes: 73 additions & 0 deletions
73
easybuild/easyconfigs/a/awscli/awscli-2.17.54-GCCcore-13.2.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| easyblock = 'PythonBundle' | ||
|
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| name = 'awscli' | ||
| version = '2.17.54' | ||
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| homepage = 'https://pypi.python.org/pypi/awscli' | ||
| description = 'Universal Command Line Environment for AWS' | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '13.2.0'} | ||
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| builddependencies = [ | ||
| ('binutils', '2.40'), | ||
| ('CMake', '3.27.6'), # required for awscrt | ||
| ] | ||
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| dependencies = [ | ||
| ('Python', '3.11.5'), | ||
| ('PyYAML', '6.0.1'), | ||
| ('ruamel.yaml', '0.18.6'), | ||
| ] | ||
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| use_pip = True | ||
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| exts_list = [ | ||
| ('jmespath', '1.0.1', { | ||
| 'source_tmpl': SOURCE_PY3_WHL, | ||
| 'checksums': ['02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980'], | ||
| }), | ||
| ('botocore', '1.35.22', { | ||
| 'source_tmpl': SOURCE_PY3_WHL, | ||
| 'checksums': ['d9bc656e7dde0b3e3f3080fc54bacff6a97fd7806b98acbcc21c7f9d4d0102b9'], | ||
| }), | ||
| ('s3transfer', '0.10.2', { | ||
| 'source_tmpl': SOURCE_PY3_WHL, | ||
| 'checksums': ['eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69'], | ||
| }), | ||
| ('prompt_toolkit', '3.0.47', { | ||
| 'source_tmpl': SOURCE_PY3_WHL, | ||
| 'checksums': ['0d7bfa67001d5e39d02c224b663abc33687405033a8c422d0d675a5a13361d10'], | ||
| }), | ||
| ('distro', '1.9.0', { | ||
| 'source_tmpl': SOURCE_PY3_WHL, | ||
| 'checksums': ['7bffd925d65168f85027d8da9af6bddab658135b840670a223589bc0c8ef02b2'], | ||
| }), | ||
| ('awscrt', '0.21.5', { | ||
| 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", | ||
| 'checksums': ['7ec2a67af30fbf386494df00bbdf996f7024000df6b01ab160014afef2b91005'], | ||
| }), | ||
| # older version of `urllib3` to avoid `ImportError: cannot import name 'DEFAULT_CIPHERS' from 'urllib3.util.ssl_'` | ||
| # see https://github.com/aws/aws-cli/issues/7905#issuecomment-1559817550 | ||
| ('urllib3', '1.26.20', { | ||
| 'source_tmpl': SOURCE_WHL, | ||
| 'checksums': ['0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e'], | ||
| }), | ||
| (name, version, { | ||
| # version requirements are too strict | ||
| 'preinstallopts': """sed -i 's/>[^"]*//g' pyproject.toml && """, | ||
| 'source_tmpl': '%(version)s.tar.gz', | ||
| 'source_urls': ['https://github.com/aws/aws-cli/archive/'], | ||
| 'checksums': ['c0a37eeb52b7df336e117667b67a275929701e9f6dad0ddb7de59a6f834e5b48'], | ||
| }), | ||
| ] | ||
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| sanity_pip_check = True | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/aws'], | ||
| 'dirs': ['lib/python%(pyshortver)s/site-packages/'], | ||
| } | ||
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| sanity_check_commands = ["aws help"] | ||
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| moduleclass = 'tools' |
68 changes: 68 additions & 0 deletions
68
easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.9-foss-2023b.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| easyblock = 'PythonPackage' | ||
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| name = 'BiG-SCAPE' | ||
| version = '1.1.9' | ||
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| homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' | ||
| description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters | ||
| (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene | ||
| cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2023b'} | ||
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| github_account = 'medema-group' | ||
| source_urls = [GITHUB_SOURCE] | ||
| sources = ['v%(version)s.tar.gz'] | ||
| patches = [ | ||
| 'BiG-SCAPE-1.1.5_use_env_var_for_html.patch', | ||
| 'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch', | ||
| ] | ||
| checksums = [ | ||
| {'v1.1.9.tar.gz': 'ef0ddb5b433e0b1467ae5f96037fd6d23ebcba6bc08201d1421eba35d072e534'}, | ||
| {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, | ||
| {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': | ||
| 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, | ||
| ] | ||
|
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| dependencies = [ | ||
| ('Python', '3.11.5'), | ||
| ('SciPy-bundle', '2023.11'), | ||
| ('Biopython', '1.84'), | ||
| ('scikit-learn', '1.4.0'), | ||
| ('networkx', '3.2.1'), | ||
| ('HMMER', '3.4'), | ||
| ('FastTree', '2.1.11'), | ||
| ] | ||
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| use_pip = True | ||
| download_dep_fail = True | ||
| sanity_pip_check = True | ||
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| options = {'modulename': 'bigscape'} | ||
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| local_lib_py_bigscape_path = 'lib/python%(pyshortver)s/site-packages/bigscape' | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/bigscape'], | ||
| 'dirs': [local_lib_py_bigscape_path], | ||
| } | ||
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| sanity_check_commands = [ | ||
| 'bigscape --help', | ||
| ] | ||
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| modextravars = { | ||
| 'BIG_SCAPE_HTML_PATH': '%(installdir)s/' + local_lib_py_bigscape_path, | ||
| } | ||
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| 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 += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " | ||
| modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" | ||
| modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " | ||
| modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " | ||
| modloadmsg += "it will use the directory where the bigscape command is started from.\n" | ||
| modloadmsg += "One can copy the domains_color_file.tsv from " | ||
| modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" | ||
|
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| moduleclass = 'bio' |
32 changes: 32 additions & 0 deletions
32
easybuild/easyconfigs/b/Biotite/Biotite-0.41.0-gfbf-2023a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| easyblock = 'PythonBundle' | ||
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| name = 'Biotite' | ||
| version = '0.41.0' | ||
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| homepage = 'https://www.biotite-python.org/' | ||
| description = """Biotite is your Swiss army knife for bioinformatics. Whether you want to | ||
| identify homologous sequence regions in a protein family or you would like to | ||
| find disulfide bonds in a protein structure: Biotite has the right tool for | ||
| you. This package bundles popular tasks in computational molecular biology into | ||
| a uniform Python library.""" | ||
|
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| toolchain = {'name': 'gfbf', 'version': '2023a'} | ||
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| dependencies = [ | ||
| ('Python', '3.11.3'), | ||
| ('Python-bundle-PyPI', '2023.06'), | ||
| ('SciPy-bundle', '2023.07'), | ||
| ('networkx', '3.1'), | ||
| ] | ||
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| use_pip = True | ||
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| exts_list = [ | ||
| ('biotite', version, { | ||
| 'checksums': ['a5fddb4d738291772735cf04dfa8b642e0bdd6b4c2c0c71e2db727c0a66bd106'], | ||
| }), | ||
| ] | ||
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| sanity_pip_check = True | ||
|
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| moduleclass = 'bio' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| easyblock = 'ConfigureMake' | ||
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| name = 'CAMPARI' | ||
| version = '4.0' | ||
| _date = '12202020' | ||
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| homepage = 'http://campari.sourceforge.net/V4/index.html' | ||
| description = """ | ||
| CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological | ||
| relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte | ||
| Carlo and molecular dynamics in seamless fashion.""" | ||
|
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| toolchain = {'name': 'foss', 'version': '2023a'} | ||
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| source_urls = [SOURCEFORGE_SOURCE] | ||
| sources = ['campari_v%s_%s.zip' % (version.split('.')[0], _date)] | ||
| checksums = ['bc627fb286b5461a5c68aa3e1a551ecd81016495163685800163c734f7c4f1bd'] | ||
|
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| builddependencies = [ | ||
| ('Autotools', '20220317'), | ||
| ] | ||
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| dependencies = [ | ||
| ('netCDF-Fortran', '4.6.1'), | ||
| ('libtirpc', '1.3.3'), | ||
| ] | ||
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| start_dir = 'source' | ||
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| # remove hardcoded paths in configure script | ||
| preconfigopts = 'sed -i "s|/usr/share|$EBROOTAUTOMAKE/share|" configure &&' | ||
| # ignore default compiler settings and use EB build environment | ||
| local_fcflags = '$FCFLAGS -fallow-argument-mismatch $CPPFLAGS' | ||
| configopts = '--enable-compiler=ignore --with-trailing-user-fcflags="%s" ' % local_fcflags | ||
| configopts += '--enable-mpi=auto ' | ||
| configopts += 'LIBS="$LIBS $LIBFFT $LIBBLAS -ltirpc"' | ||
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| buildopts = 'all' | ||
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| maxparallel = 10 | ||
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| postinstallcmds = ['cp -a %(builddir)s/campari/{data,doc,examples,params,tools,LICENSE} %(installdir)s/'] | ||
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| _binaries = ['campari', 'campari_mpi', 'campari_mpi_threads', 'campari_threads', 'camp_ncminer', 'camp_ncminer_threads'] | ||
| _libraries = ['lcampari.a', 'lcampari_mpi.a', 'lcampari_mpi_threads.a', 'lcampari_threads.a', 'libxdrf.a'] | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/%s' % x for x in _binaries] + ['lib/%s' % x for x in _libraries], | ||
| 'dirs': [], | ||
| } | ||
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| sanity_check_commands = ['campari -h | grep "USAGE: CAMPARI"'] | ||
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| moduleclass = 'bio' |
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