From 8a9f2ac1c725754588036017bb54c738d5fe6a3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Mar 2023 00:05:31 +0100 Subject: [PATCH] adding easyconfigs: CellOracle-0.12.0-foss-2022a.eb, GimmeMotifs-0.17.2-foss-2022a.eb, qnorm-0.8.1-foss-2022a.eb, Qtconsole-5.4.0-GCCcore-11.3.0.eb --- .../CellOracle-0.12.0-foss-2022a.eb | 59 ++++++++++++++ .../GimmeMotifs-0.17.2-foss-2022a.eb | 77 +++++++++++++++++++ .../Qtconsole-5.4.0-GCCcore-11.3.0.eb | 31 ++++++++ .../q/qnorm/qnorm-0.8.1-foss-2022a.eb | 36 +++++++++ 4 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb new file mode 100644 index 00000000000..e712870108d --- /dev/null +++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'CellOracle' +version = '0.12.0' + +homepage = 'https://github.com/morris-lab/CellOracle' +description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data +and Gene Regulatory Network models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('R', '4.2.1'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('velocyto', '0.17.17'), + ('umap-learn', '0.5.3'), + ('Arrow', '8.0.0'), + ('tqdm', '4.64.0'), + ('igraph', '0.10.3'), + ('IPython', '8.5.0'), + ('scanpy', '1.9.1'), + ('GOATOOLS', '1.3.1'), + ('genomepy', '0.15.0'), + ('GimmeMotifs', '0.17.2'), + ('Qtconsole', '5.4.0'), +] + +use_pip = True + +# remove louvain from requirements, since CellOracle doesn't actually use it at all +local_preinstallopts = "sed -i '/louvain/d' requirements.txt && " +# drop strict version requirement for gimmemotifs dependency +local_preinstallopts += "sed -i 's/gimmemotifs.*/gimmemotifs/g' requirements.txt && " + +exts_list = [ + ('jupyter-console', '6.4.4', { + 'sources': ['jupyter_console-%(version)s.tar.gz'], + 'checksums': ['172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('celloracle', version, { + 'checksums': ['9d533ee3e8c14828b6859ea195e92d184b050b0782fee430eda3b01359a564d5'], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb new file mode 100644 index 00000000000..a57ae34779f --- /dev/null +++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'GimmeMotifs' +version = '0.17.2' + +homepage = 'https://github.com/vanheeringen-lab/gimmemotifs' +description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('pybedtools', '0.9.0'), + ('Pysam', '0.19.1'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), + ('statsmodels', '0.13.1'), + ('tqdm', '4.64.0'), + ('genomepy', '0.15.0'), + ('qnorm', '0.8.1'), + ('Arrow', '8.0.0'), # provides pyarrow, required by feather-format + ('HTSeq', '2.0.2'), # required by biofluff + ('pyBigWig', '0.3.18'), # required by biofluff +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('biofluff', '3.0.4', { + 'modulename': 'fluff', + 'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'], + }), + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('iteround', '1.0.4', { + 'source_urls': ['https://github.com/cgdeboer/iteround/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('loguru', '0.6.0', { + 'checksums': ['066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c'], + }), + ('xxhash', '3.2.0', { + 'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'], + }), + ('xdg', '6.0.0', { + 'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'], + }), + ('gimmemotifs', version, { + 'preinstallopts': """sed -i '/"configparser"/d' setup.py && """, + 'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gimme'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gimme --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4ca3e9f8a2e --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.4.0' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['57748ea2fd26320a0b77adba20131cfbb13818c7c96d83fafcb110ff55f58b35'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('QtPy', '2.3.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb new file mode 100644 index 00000000000..1b0932b22af --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), +] + +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'