From bbe4e609d2b9d1cae8fb9ea11de89cbeaf6d3cc5 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 3 Jan 2025 18:32:43 +0100 Subject: [PATCH] adding easyconfigs: pydot-3.0.3-GCCcore-13.3.0.eb, XlsxWriter-3.2.0-GCCcore-13.3.0.eb, openpyxl-3.1.5-GCCcore-13.3.0.eb, GOATOOLS-1.4.12-foss-2024a.eb --- .../g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb | 72 +++++++++++++++++++ .../openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb | 35 +++++++++ .../p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb | 28 ++++++++ .../XlsxWriter-3.2.0-GCCcore-13.3.0.eb | 34 +++++++++ 4 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb new file mode 100644 index 00000000000..ba3ae7b8125 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.12-foss-2024a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Pavel Tománek (Inuits) + +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.4.12' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2024a'} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '8.7.1')] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('XlsxWriter', '3.2.0'), + ('statsmodels', '0.14.4'), + ('pydot', '3.0.3'), + ('openpyxl', '3.1.5'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('ftpretty', '0.4.0', { + 'checksums': ['61233b9212f2cceec96ee2c972738fa31cae7248e92d0874c99c04ee739bb5a9'], + }), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..9242d1fedf5 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.5-GCCcore-13.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.1.5' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('lxml', '5.3.0'), + ('Pillow', '10.4.0'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '2.0.0', { + 'checksums': ['dab3f4764309081ce75662649be815c4c9081e88f0837825f90fd28317d4da54'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['cf0e3cf56142039133628b5acffe8ef0c12bc902d2aadd3e0fe5878dc08d1050'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e304bbecc1a --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-3.0.3-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '3.0.3' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +exts_list = [ + (name, version, { + 'checksums': ['5e009d97b2fff92b7a88f09ec1fd5b163f07f3b10469c927d362471d6faa0d50'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..8c54c8caada --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.2.0-GCCcore-13.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.2.0' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9977d0c661a72866a61f9f7a809e25ebbb0fb7036baa3b9fe74afcfca6b3cb8c'] + +builddependencies = [ + ('binutils', '2.42'), +] + +dependencies = [ + ('Python', '3.12.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools'