diff --git a/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb new file mode 100644 index 00000000..12ab815b --- /dev/null +++ b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb @@ -0,0 +1,75 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'MacSyFinder' +version = '2.1.6' + +homepage = "https://github.com/gem-pasteur/macsyfinder" +description = """MacSyFinder - Detection of macromolecular systems in protein datasets + using systems modelling and similarity search""" +citing = """MacSyFinder v2: Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; + Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S. MacSyFinder v2: + Improved modelling and search engine to identify molecular systems in genomes. + Peer Community Journal, Volume 3 (2023), article no. e28. + doi : 10.24072/pcjournal.250. https://peercommunityjournal.org/articles/10.24072/pcjournal.250/""" + +toolchain = {'name': 'foss', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('HMMER', '3.4'), + ('GitPython', '3.1.43'), # for macsylib[model] + ('lxml', '5.3.0'), # for macsylyb[model] + ('networkx', '3.4.2'), + ('PyYAML', '6.0.2'), + ('SciPy-bundle', '2024.05'), + ('flit', '3.9.0'), + +] + +exts_list = [ + ('colorlog', '6.9.0', { + 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], + }), + ('macsylib', '1.0.4', { + 'patches': ['%(name)s-%(version)s_licence.patch'], + 'use_pip_extras': 'model', + 'testinstall': True, + # 'runtest': '%(python)s -m unittest discover -vv', # fails to resolve in _pre_sanity_check_hook + 'runtest': 'python -m unittest discover -vv', + 'checksums': [ + {'macsylib-1.0.4.tar.gz': '084cf0ff7c89642d925bd1457f6ed32089d0be50b8ad726c5d75026efa438abb'}, + {'macsylib-1.0.4_licence.patch': 'e6b67d40815b3910f5f6d72499f4d1cea96f113c580e061325cba70bb2555d45'}, + ], + }), + ('macsyfinder', version, { + 'patches': ['%(name)s-%(version)s_licence.patch'], + 'use_pip_extras': 'model', + 'testinstall': True, + # 'runtest': '%(python)s -m unittest discover -vv', # fails to resolve template python_cmd + 'runtest': 'python -m unittest discover -vv', + 'checksums': [ + {'macsyfinder-2.1.6.tar.gz': 'd05f5eb46b03c62e2183111225aa869a97ca1e4353c07fe342ac28be22cd523e'}, + {'macsyfinder-2.1.6_licence.patch': 'f67604332e40c30287dbd58fa2aad0c77fd169e4e861cb18f56adf9548657a9b'}, + ], + }), +] + +sanity_check_paths = { + 'files': [ + 'bin/macsyconfig', + 'bin/macsydata', + 'bin/macsyfinder', + 'bin/macsyprofile', + 'bin/msf_config', + 'bin/msf_data', + 'bin/msf_merge', + 'bin/msf_profile', + 'bin/msf_split', + 'bin/msl_data', + ], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/'] +} + + +moduleclass = 'bio' diff --git a/easyconfigs/m/MacSyFinder/macsyfinder-2.1.6_licence.patch b/easyconfigs/m/MacSyFinder/macsyfinder-2.1.6_licence.patch new file mode 100644 index 00000000..66314acb --- /dev/null +++ b/easyconfigs/m/MacSyFinder/macsyfinder-2.1.6_licence.patch @@ -0,0 +1,14 @@ +diff --git a/pyproject.toml b/pyproject.toml +index 324447b6..91387a75 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -15,8 +15,7 @@ maintainers = [ + description = 'MacSyFinder: Detection of macromolecular systems in protein datasets using systems modelling and similarity search' + keywords = ['science', 'research', 'bioinformatic', 'microbiology', 'genomic', 'prokaryote', 'functional gene annotation'] + readme = "README.md" +-license = "GPL-3.0-or-later" +-license-files = ["COPYING"] ++license = {file = 'COPYING'} + + classifiers = [ + "Programming Language :: Python :: 3", diff --git a/easyconfigs/m/MacSyFinder/macsylib-1.0.4_licence.patch b/easyconfigs/m/MacSyFinder/macsylib-1.0.4_licence.patch new file mode 100644 index 00000000..69b68a7b --- /dev/null +++ b/easyconfigs/m/MacSyFinder/macsylib-1.0.4_licence.patch @@ -0,0 +1,14 @@ +diff --git a/pyproject.toml b/pyproject.toml +index a60ff60..15d9a5b 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -15,8 +15,7 @@ maintainers = [ + description = 'MacSyLib: Python library that help to detect of macromolecular, systems genetic pathways… in prokaryotes protein datasets using systems modelling and similarity search.' + keywords = ['science', 'research', 'bioinformatic', 'microbiology', 'genomic', 'prokaryote', 'functional gene annotation'] + readme = "README.md" +-license = 'GPL-3.0-or-later' +-license-files = ["COPYING"] ++license = {file = "COPYING"} + + classifiers = [ + "Programming Language :: Python :: 3",