From 10702f4f6b2fb7ffefd56574b40956376d8213a4 Mon Sep 17 00:00:00 2001 From: Vladislav Mogilev Date: Thu, 29 Jan 2026 14:17:41 +0000 Subject: [PATCH 1/3] build(MacSyFinder): :white_check_mark: 2.1.6 --- .../MacSyFinder-2.1.6-foss-2024a.eb | 57 +++++++++++++++++++ .../macsyfinder-2.1.6_licence.patch | 14 +++++ .../MacSyFinder/macsylib-1.0.4_licence.patch | 14 +++++ 3 files changed, 85 insertions(+) create mode 100644 easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb create mode 100644 easyconfigs/m/MacSyFinder/macsyfinder-2.1.6_licence.patch create mode 100644 easyconfigs/m/MacSyFinder/macsylib-1.0.4_licence.patch 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..403b3c79 --- /dev/null +++ b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb @@ -0,0 +1,57 @@ +# 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'), + +] + +#source_urls = [PYPI_SOURCE] +#sources = [SOURCE_TAR_GZ] + +exts_list = [ + ('colorlog', '6.9.0', { + 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], + }), + ('macsylib', '1.0.4', { + 'patches': ['%(name)s-%(version)s_licence.patch'], + 'use_pip_extras': 'model', + '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', + 'checksums': [ + {'macsyfinder-2.1.6.tar.gz': 'd05f5eb46b03c62e2183111225aa869a97ca1e4353c07fe342ac28be22cd523e'}, + {'macsyfinder-2.1.6_licence.patch': 'f67604332e40c30287dbd58fa2aad0c77fd169e4e861cb18f56adf9548657a9b'}, + ], + }), +] + +#sanity_ + +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", From 04ad8db13877d6a44299e5de3726ef7c4b187f0f Mon Sep 17 00:00:00 2001 From: Vladislav Mogilev Date: Thu, 29 Jan 2026 16:39:12 +0000 Subject: [PATCH 2/3] test(MacSyFinder): unittests --- .../MacSyFinder-2.1.6-foss-2024a.eb | 26 ++++++++++++++++--- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb index 403b3c79..51d6b7a5 100644 --- a/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb +++ b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb @@ -27,9 +27,6 @@ dependencies = [ ] -#source_urls = [PYPI_SOURCE] -#sources = [SOURCE_TAR_GZ] - exts_list = [ ('colorlog', '6.9.0', { 'checksums': ['bfba54a1b93b94f54e1f4fe48395725a3d92fd2a4af702f6bd70946bdc0c6ac2'], @@ -37,6 +34,9 @@ exts_list = [ ('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'}, @@ -45,6 +45,9 @@ exts_list = [ ('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'}, @@ -52,6 +55,21 @@ exts_list = [ }), ] -#sanity_ +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' From 7924df6a8a1b812467ce76c18bca333210368bc2 Mon Sep 17 00:00:00 2001 From: Vladislav Mogilev Date: Thu, 29 Jan 2026 16:43:05 +0000 Subject: [PATCH 3/3] style(MacSyFinder): :pencil2: trailing whitespaces --- easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb index 51d6b7a5..12ab815b 100644 --- a/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb +++ b/easyconfigs/m/MacSyFinder/MacSyFinder-2.1.6-foss-2024a.eb @@ -19,11 +19,11 @@ dependencies = [ ('Python', '3.12.3'), ('HMMER', '3.4'), ('GitPython', '3.1.43'), # for macsylib[model] - ('lxml', '5.3.0'), # for macsylyb[model] + ('lxml', '5.3.0'), # for macsylyb[model] ('networkx', '3.4.2'), ('PyYAML', '6.0.2'), ('SciPy-bundle', '2024.05'), - ('flit', '3.9.0'), + ('flit', '3.9.0'), ] @@ -46,7 +46,7 @@ exts_list = [ '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)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'},