Merge pull request easybuilders#20665 from pavelToman/20240527204201_…

…new_pr_TF-COMB11

{bio}[foss/2022b] TF-COMB v1.1, TOBIAS v0.16.1, svist4get v1.3.1, ...

easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2022b.eb

@@ -0,0 +1,27 @@
+easyblock = 'PythonPackage'
+
+name = 'adjustText'
+version = '0.7.3'
+
+homepage = 'https://github.com/Phlya/adjustText'
+description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps."
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('matplotlib', '3.7.0'),
+    ('SciPy-bundle', '2023.02'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_pip_check = True
+
+options = {'modulename': 'adjustText'}
+
+moduleclass = 'tools'

easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.4.5-foss-2022b.eb

@@ -0,0 +1,73 @@
+# 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 = '1.4.5'
+
+homepage = 'https://github.com/tanghaibao/goatools'
+description = "A Python library for Gene Ontology analyses"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+# must download sources via git to preserve .git directory,
+# since setuptools-scm is used to determine version
+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', '7.86.0')]
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('XlsxWriter', '3.1.2'),
+    ('statsmodels', '0.14.0'),
+    ('pydot', '2.0.0'),
+    ('openpyxl', '3.1.2'),
+]
+
+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'

easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.2.0.eb

@@ -0,0 +1,25 @@
+# updated: Denis Kristak, Pavel Tománek (INUITS)
+easyblock = 'PythonBundle'
+
+name = 'pydot'
+version = '2.0.0'
+
+homepage = 'https://github.com/pydot/pydot'
+description = "Python interface to Graphviz's Dot language."
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [('Python', '3.10.8')]
+
+exts_list = [
+    (name, version, {
+        'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'],
+    }),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'vis'

easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022b.eb

@@ -0,0 +1,25 @@
+easyblock = 'PythonPackage'
+
+name = 'python-louvain'
+version = '0.16'
+
+homepage = 'https://pypi.org/project/python-louvain'
+description = "Louvain algorithm for community detection"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b']
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('networkx', '3.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'community'}
+
+moduleclass = 'lib'

easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022b.eb

@@ -0,0 +1,36 @@
+easyblock = 'PythonPackage'
+
+name = 'qnorm'
+version = '0.8.1'
+
+homepage = 'https://github.com/Maarten-vd-Sande/qnorm'
+description = "Fast-ish (and correct!) quantile normalization in Python"
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('numba', '0.58.1'),
+]
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7']
+
+download_dep_fail = True
+use_pip = True
+
+# pyproject.toml included in qnorm source tarball does not include standard fields,
+# it's only there to be read by setup.py...
+preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && "
+
+sanity_check_paths = {
+    'files': ['bin/qnorm'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["qnorm --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2022b.eb

@@ -0,0 +1,61 @@
+# Author: J. Sassmannshausen (Imperial College London/UK)
+# Update: Pavel Tománek (Inuits)
+
+easyblock = 'PythonBundle'
+
+name = 'svist4get'
+version = '1.3.1'
+
+homepage = 'https://github.com/art-egorov/svist4get'
+description = """Svist4get is a simple bioinformatics tool for visualization of 
+genomic signal tracks in user-defined genomic windows, either arbitrary selected 
+by genomic coordinates or anchored to particular transcripts or genes."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('pybedtools', '0.9.0'),
+    ('Biopython', '1.81'),
+    ('Pillow', '9.4.0'),
+    ('ImageMagick', '7.1.0-53'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('reportlab', '3.6.9', {
+        'patches': ['reportlab-3.6.12-fontconfig.patch'],
+        'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84',
+                      # reportlab-3.6.12-fontconfig.patch:
+                      '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'],
+    }),
+    ('configs', '3.0.3', {
+        'sources': ['%(name)s-%(version)s.zip'],
+        'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'],
+    }),
+    ('argparse', '1.4.0', {
+        'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'],
+    }),
+    ('Wand', '0.6.10', {
+        'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'],
+    }),
+    (name, version, {
+        # unpin statistics dependency - it is old package and interfering with python lib statistics
+        'preinstallopts': "sed -i 's/statistics//' setup.py && ",
+        'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/svist4get', 'bin/svist4get_copier'],
+    'dirs': ['lib'],
+}
+
+sanity_check_commands = [
+    "svist4get --help",
+    "svist4get -v",
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/TF-COMB/TF-COMB-1.1-foss-2022b.eb

@@ -0,0 +1,48 @@
+easyblock = 'PythonBundle'
+
+name = 'TF-COMB'
+version = '1.1'
+
+homepage = 'https://github.com/loosolab/TF-COMB'
+description = """Transcription Factor Co-Occurrence using Market Basket analysis."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('tqdm', '4.64.1'),
+    ('Pysam', '0.21.0'),
+    ('matplotlib', '3.7.0'),
+    ('networkx', '3.0'),
+    ('Graphviz', '8.1.0'),
+    ('statsmodels', '0.14.0'),
+    ('dill', '0.3.7'),
+    ('Seaborn', '0.12.2'),
+    ('IPython', '8.14.0'),
+    ('TOBIAS', '0.16.1'),
+    ('python-louvain', '0.16'),
+    ('GOATOOLS', '1.4.5'),
+    ('qnorm', '0.8.1'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# remove graphviz from deps - the pip check failing, should be "import gv"
+local_tfcomb_preinstallopts = "sed -i '70d' setup.py && "
+# fix "import graphviz" to "import gv"
+local_tfcomb_preinstallopts += "sed -i 's/import graphviz/import gv as graphviz/' tfcomb/plotting.py && "
+
+exts_list = [
+    ('uropa', '4.0.3', {
+        'checksums': ['e0b648881b95f301e3f3ecc924314995312f10b0cbabf96d5a5ce2fb18c53a59'],
+    }),
+    (name, version, {
+        'preinstallopts': local_tfcomb_preinstallopts,
+        'modulename': 'tfcomb',
+        'checksums': ['5b718061660e0f9f94d86459eb742ca81de5851b0defd8b08c8a7a7e3370c253'],
+    }),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.16.1-foss-2022b.eb

@@ -0,0 +1,55 @@
+easyblock = 'PythonBundle'
+
+name = 'TOBIAS'
+version = '0.16.1'
+
+homepage = 'https://github.com/loosolab/TOBIAS'
+description = """TOBIAS is a collection of command-line bioinformatics tools 
+for performing footprinting analysis on ATAC-seq data."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('SciPy-bundle', '2023.02'),
+    ('matplotlib', '3.7.0'),
+    ('Seaborn', '0.12.2'),
+    ('Pysam', '0.21.0'),
+    ('pybedtools', '0.9.0'),
+    ('boto3', '1.26.163'),
+    ('pyBigWig', '0.3.22'),
+    ('scikit-learn', '1.2.1'),
+    ('PyYAML', '6.0'),
+    ('XlsxWriter', '3.1.2'),
+    ('svist4get', '1.3.1'),
+    ('adjustText', '0.7.3'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('kneed', '0.8.5', {
+        'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'],
+    }),
+    ('logomaker', '0.8', {
+        'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'],
+    }),
+    ('MOODS-python', '1.9.4.1', {
+        'modulename': 'MOODS',
+        'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'],
+    }),
+    ('PyPDF2', '3.0.1', {
+        'modulename': 'PyPDF2',
+        'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'],
+    }),
+    ('tobias', version, {
+        # remove pyBigWig dependency - pip_check fails with "import pybigwig"
+        'preinstallopts': "sed -i '81d' setup.py && ",
+        'checksums': ['c46267c01287be06201b3e6f7a36daad1ad86d6c578f96e878501be7da7fd109'],
+    }),
+]
+
+sanity_check_commands = ["python -c 'import pyBigWig'"]
+
+moduleclass = 'bio'