From 4806d8e56d6058b17b3c6e83d31b6a3c127a0176 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 18 Jul 2024 16:13:12 +0200 Subject: [PATCH] #64 update to 2023a + fill all deps --- .../MACS2-2.2.9.1-foss-2022a.eb | 0 .../Sphinx-RTD-Theme-1.1.1-GCCcore-11.3.0.eb | 0 .../{ => old_from_Denis}/adjust_text.eb | 0 .../{ => old_from_Denis}/bioservices.eb | 0 .../cattrs-23.1.2-simplify_pyproject.patch | 0 ...taclasses_json-0.6.1-remove_dev_deps.patch | 0 .../gensim-4.3.2-foss-2022a.eb | 0 .../plumbum-1.8.2-dont_use_hatchling.patch | 0 .../pycisTopic-1.0.2-manual_versioning.patch | 0 .../pycistarget-1.0.2-manual_versioning.patch | 0 .../pyfasta-0.5.2-foss-2022a.eb | 0 .../pyfasta-0.5.2-resolve_deprecated.patch | 0 .../pygam-0.9.0-simplify_pyproject.patch | 0 ...n-Levenshtein-0.22.0-add_python_exec.patch | 0 .../python-Levenshtein-0.22.0-foss-2022a.eb | 0 .../{ => old_from_Denis}/rapidfuzz.eb | 0 .../requests-cache-1.1.0-fix_deps.patch | 0 .../scenicplus-1.0.0-manual_versioning.patch | 0 .../{ => old_from_Denis}/scenicplus.eb | 0 64_scenicplus/scenicplus-2023a.eb | 225 ++++++++++++++++++ 20 files changed, 225 insertions(+) rename 64_scenicplus/{ => old_from_Denis}/MACS2-2.2.9.1-foss-2022a.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/Sphinx-RTD-Theme-1.1.1-GCCcore-11.3.0.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/adjust_text.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/bioservices.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/cattrs-23.1.2-simplify_pyproject.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/dataclasses_json-0.6.1-remove_dev_deps.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/gensim-4.3.2-foss-2022a.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/plumbum-1.8.2-dont_use_hatchling.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/pycisTopic-1.0.2-manual_versioning.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/pycistarget-1.0.2-manual_versioning.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/pyfasta-0.5.2-foss-2022a.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/pyfasta-0.5.2-resolve_deprecated.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/pygam-0.9.0-simplify_pyproject.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/python-Levenshtein-0.22.0-add_python_exec.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/python-Levenshtein-0.22.0-foss-2022a.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/rapidfuzz.eb (100%) rename 64_scenicplus/{ => old_from_Denis}/requests-cache-1.1.0-fix_deps.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/scenicplus-1.0.0-manual_versioning.patch (100%) rename 64_scenicplus/{ => old_from_Denis}/scenicplus.eb (100%) create mode 100644 64_scenicplus/scenicplus-2023a.eb diff --git a/64_scenicplus/MACS2-2.2.9.1-foss-2022a.eb b/64_scenicplus/old_from_Denis/MACS2-2.2.9.1-foss-2022a.eb similarity index 100% rename from 64_scenicplus/MACS2-2.2.9.1-foss-2022a.eb rename to 64_scenicplus/old_from_Denis/MACS2-2.2.9.1-foss-2022a.eb diff --git a/64_scenicplus/Sphinx-RTD-Theme-1.1.1-GCCcore-11.3.0.eb b/64_scenicplus/old_from_Denis/Sphinx-RTD-Theme-1.1.1-GCCcore-11.3.0.eb similarity index 100% rename from 64_scenicplus/Sphinx-RTD-Theme-1.1.1-GCCcore-11.3.0.eb rename to 64_scenicplus/old_from_Denis/Sphinx-RTD-Theme-1.1.1-GCCcore-11.3.0.eb diff --git a/64_scenicplus/adjust_text.eb b/64_scenicplus/old_from_Denis/adjust_text.eb similarity index 100% rename from 64_scenicplus/adjust_text.eb rename to 64_scenicplus/old_from_Denis/adjust_text.eb diff --git a/64_scenicplus/bioservices.eb b/64_scenicplus/old_from_Denis/bioservices.eb similarity index 100% rename from 64_scenicplus/bioservices.eb rename to 64_scenicplus/old_from_Denis/bioservices.eb diff --git a/64_scenicplus/cattrs-23.1.2-simplify_pyproject.patch b/64_scenicplus/old_from_Denis/cattrs-23.1.2-simplify_pyproject.patch similarity index 100% rename from 64_scenicplus/cattrs-23.1.2-simplify_pyproject.patch rename to 64_scenicplus/old_from_Denis/cattrs-23.1.2-simplify_pyproject.patch diff --git a/64_scenicplus/dataclasses_json-0.6.1-remove_dev_deps.patch b/64_scenicplus/old_from_Denis/dataclasses_json-0.6.1-remove_dev_deps.patch similarity index 100% rename from 64_scenicplus/dataclasses_json-0.6.1-remove_dev_deps.patch rename to 64_scenicplus/old_from_Denis/dataclasses_json-0.6.1-remove_dev_deps.patch diff --git a/64_scenicplus/gensim-4.3.2-foss-2022a.eb b/64_scenicplus/old_from_Denis/gensim-4.3.2-foss-2022a.eb similarity index 100% rename from 64_scenicplus/gensim-4.3.2-foss-2022a.eb rename to 64_scenicplus/old_from_Denis/gensim-4.3.2-foss-2022a.eb diff --git a/64_scenicplus/plumbum-1.8.2-dont_use_hatchling.patch b/64_scenicplus/old_from_Denis/plumbum-1.8.2-dont_use_hatchling.patch similarity index 100% rename from 64_scenicplus/plumbum-1.8.2-dont_use_hatchling.patch rename to 64_scenicplus/old_from_Denis/plumbum-1.8.2-dont_use_hatchling.patch diff --git a/64_scenicplus/pycisTopic-1.0.2-manual_versioning.patch b/64_scenicplus/old_from_Denis/pycisTopic-1.0.2-manual_versioning.patch similarity index 100% rename from 64_scenicplus/pycisTopic-1.0.2-manual_versioning.patch rename to 64_scenicplus/old_from_Denis/pycisTopic-1.0.2-manual_versioning.patch diff --git a/64_scenicplus/pycistarget-1.0.2-manual_versioning.patch b/64_scenicplus/old_from_Denis/pycistarget-1.0.2-manual_versioning.patch similarity index 100% rename from 64_scenicplus/pycistarget-1.0.2-manual_versioning.patch rename to 64_scenicplus/old_from_Denis/pycistarget-1.0.2-manual_versioning.patch diff --git a/64_scenicplus/pyfasta-0.5.2-foss-2022a.eb b/64_scenicplus/old_from_Denis/pyfasta-0.5.2-foss-2022a.eb similarity index 100% rename from 64_scenicplus/pyfasta-0.5.2-foss-2022a.eb rename to 64_scenicplus/old_from_Denis/pyfasta-0.5.2-foss-2022a.eb diff --git a/64_scenicplus/pyfasta-0.5.2-resolve_deprecated.patch b/64_scenicplus/old_from_Denis/pyfasta-0.5.2-resolve_deprecated.patch similarity index 100% rename from 64_scenicplus/pyfasta-0.5.2-resolve_deprecated.patch rename to 64_scenicplus/old_from_Denis/pyfasta-0.5.2-resolve_deprecated.patch diff --git a/64_scenicplus/pygam-0.9.0-simplify_pyproject.patch b/64_scenicplus/old_from_Denis/pygam-0.9.0-simplify_pyproject.patch similarity index 100% rename from 64_scenicplus/pygam-0.9.0-simplify_pyproject.patch rename to 64_scenicplus/old_from_Denis/pygam-0.9.0-simplify_pyproject.patch diff --git a/64_scenicplus/python-Levenshtein-0.22.0-add_python_exec.patch b/64_scenicplus/old_from_Denis/python-Levenshtein-0.22.0-add_python_exec.patch similarity index 100% rename from 64_scenicplus/python-Levenshtein-0.22.0-add_python_exec.patch rename to 64_scenicplus/old_from_Denis/python-Levenshtein-0.22.0-add_python_exec.patch diff --git a/64_scenicplus/python-Levenshtein-0.22.0-foss-2022a.eb b/64_scenicplus/old_from_Denis/python-Levenshtein-0.22.0-foss-2022a.eb similarity index 100% rename from 64_scenicplus/python-Levenshtein-0.22.0-foss-2022a.eb rename to 64_scenicplus/old_from_Denis/python-Levenshtein-0.22.0-foss-2022a.eb diff --git a/64_scenicplus/rapidfuzz.eb b/64_scenicplus/old_from_Denis/rapidfuzz.eb similarity index 100% rename from 64_scenicplus/rapidfuzz.eb rename to 64_scenicplus/old_from_Denis/rapidfuzz.eb diff --git a/64_scenicplus/requests-cache-1.1.0-fix_deps.patch b/64_scenicplus/old_from_Denis/requests-cache-1.1.0-fix_deps.patch similarity index 100% rename from 64_scenicplus/requests-cache-1.1.0-fix_deps.patch rename to 64_scenicplus/old_from_Denis/requests-cache-1.1.0-fix_deps.patch diff --git a/64_scenicplus/scenicplus-1.0.0-manual_versioning.patch b/64_scenicplus/old_from_Denis/scenicplus-1.0.0-manual_versioning.patch similarity index 100% rename from 64_scenicplus/scenicplus-1.0.0-manual_versioning.patch rename to 64_scenicplus/old_from_Denis/scenicplus-1.0.0-manual_versioning.patch diff --git a/64_scenicplus/scenicplus.eb b/64_scenicplus/old_from_Denis/scenicplus.eb similarity index 100% rename from 64_scenicplus/scenicplus.eb rename to 64_scenicplus/old_from_Denis/scenicplus.eb diff --git a/64_scenicplus/scenicplus-2023a.eb b/64_scenicplus/scenicplus-2023a.eb new file mode 100644 index 00000000..32578639 --- /dev/null +++ b/64_scenicplus/scenicplus-2023a.eb @@ -0,0 +1,225 @@ +easyblock = 'PythonBundle' + +name = 'scenicplus' +version = '1.0.0-18072023' +local_commit = "fa55dae" + +homepage = 'https://github.com/aertslab/scenicplus' +description = """SCENIC+ is a python package to build gene regulatory networks (GRNs) +using combined or separate single-cell gene expression (scRNA-seq) and single-cell +chromatin accessibility (scATAC-seq) data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# DEPS: + # ok pycistarget @ git+https://github.com/aertslab/pycistarget + # ok pycisTopic @ git+https://github.com/aertslab/pycisTopic + # ok loomxpy + # OK pyscenic in sc-bundle + # ?OK adjustText==1.0.4 in sc-bundle + # OK anndata==0.10.5.post1 + # ok annoy==1.17.3 + # OK arboreto==0.1.6 in pyScenic + # ok attr==0.3.2 + # ok attrs==23.2.0 in pypi bundle 23.1.0 + # OK bbknn==1.6.0 in sc-bundle + # ?OK beautifulsoup4==4.12.3 have 4.12.2 + # bs4==0.0.2 -> it is only dummy -> delete from deps + # OK ctxcore==0.2.0 in pyScenic + # ?OK Cython==0.29.37 in pypi-bundle is v0.29.35 + # OK cytoolz==0.12.3 in pyScenic + # ?OK dask==2024.2.1 in pyScenic v2023.9.2 + # ?OK dill==0.3.8 in pyScenic v0.3.7 + # -> gensim==4.3.2 -> UPDATE + # ok gseapy==0.10.8 + # ?OK h5py==3.10.0 have v3.9.0 + # OK harmonypy==0.0.9 in sc-bundle + # OK igraph==0.11.4 + # ?OK imageio==2.34.0 have v2.33.1 + # OK importlib-metadata==7.0.1 pypi bundle + # OK importlib_resources==6.1.2 pypi bundle + # OK intervaltree==3.1.0 pypi bundle + # OK joblib==1.3.2 pypi bundle + # -> kaleido==0.2.1 -> UPDATE + # ok lda==3.0.0 + # OK leidenalg==0.10.2 + # ?OK lxml==5.1.0 have v4.9.2 + # OK MACS2==2.2.9.1 + # OK matplotlib==3.6.3 in sc-bundle + # OK mudata==0.2.3 in sc-bundle + # ok ncls==0.0.68 + # ?OK networkx==3.2.1 have v3.1 in pyScenic + # ?OK numba==0.59.0 have v0.58.1 + # -> numexpr==2.9.0 -> UPDATE + # ?OK numpy==1.26.4 have v1.25.1 + # OK numpy-groupies==0.10.2 in loompy + # ?OK pandas==1.5.0 have 2.0.3 + # ?OK plotly==5.19.0 have v5.16.0 + # OK plotnine==0.12.4 in sc-bundle + # ?OK polars==0.20.13 have v0.20.2 + # ?OK pyarrow==15.0.0 have v14.0.1 + # OK pyarrow-hotfix==0.6 -> not needed for Arrow 14.0.1 + # OK pybedtools==0.9.1 + # ok pybigtools==0.1.2 + # OK pyBigWig==0.3.22 + # ok pybiomart==0.2.0 + # -> pyfasta==0.5.2 -> UPDATE + # OK pygam==0.9.0 + # ok pyranges==0.0.111 + # ok pyrle==0.0.39 + # OK pysam==0.22.0 + # ok pyvis==0.3.2 + # ?OK ray==2.9.3 have v2.9.1 + # OK requests==2.31.0 pypi bundle + # ok requests-cache==1.2.0 + # ok scanorama==1.7.4 + # OK scanpy==1.8.2 in sc-bundle + # ok scatac_fragment_tools==0.1.0 + # OK scikit-image==0.22.0 + # ?OK scikit-learn==1.3.2 have v1.3.1 in pyScenic or for 2023a either v1.4.2 + # ?OK scipy==1.12.0 have v1.11.1 + # -> scrublet==0.2.3 -> UPDATE + # OK seaborn==0.13.2 in sc-bundle + # ?OK snakemake==8.5.5 have v8.4.2 + # ok snakemake-interface-common==1.17.1 in snakemake + # ok snakemake-interface-executor-plugins==8.2.0 in snakemake + # ok snakemake-interface-report-plugins==1.0.0 to exts + # ok snakemake-interface-storage-plugins==3.1.1 in snakemake + # ok statistics==1.0.3.5 + # OK statsmodels==0.14.1 + # ok tmtoolkit==0.12.0 + # ?OK tqdm==4.66.2 v4.66.1 in pyScenic + # ok tspex==0.6.3 + # ok typing==3.7.4.3 + # OK umap-learn==0.5.5 in pyScenic + # deps pycistarget: + # OK IPython + # ok pandoc + # -> sphinx_rtd_theme ->UPDATE + # ok nbsphinx + # ok nbsphinx_link + # ok numpydoc + # OK typing_extensions + # deps pycisTopic: + # OK ipympl + # ok pyopenssl + # -> python-Levenshtein -> UPDATE + # OK tables + # OK xlrd in pypi bundle + # ok papermill + +# builddependencies = [('poetry', '1.5.1'), ] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Single-cell-python-bundle', '2024.02'), + ('anndata', '0.10.5.post1'), + ('BeautifulSoup', '4.12.2'), + ('h5py', '3.9.0'), + ('python-igraph', '0.11.4'), + ('imageio', '2.33.1') + ('leidenalg', '0.10.2'), + ('lxml', '4.9.2'), + ('MACS2', '2.2.9.1'), + ('numba', '0.58.1'), + ('polars', '0.20.2'), + ('Arrow', '14.0.1'), + ('plotly.py', '5.16.0'), + ('pybedtools', '0.9.1'), + ('pyBigWig', '0.3.22'), + ('pyGAM', '0.9.1'), + ('Pysam', '0.22.0'), + ('Ray-project', '2.9.1'), + ('scikit-image', '0.22.0'), + ('snakemake', '8.4.2'), + ('statsmodels', '0.14.1'), + ('IPython', '8.14.0'), + ('Pandoc', '3.1.2', '', SYSTEM), + ('ipympl', '0.9.3'), + ('PyTables', '3.8.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('annoy', '1.17.3'), + ('attr', '0.3.2'), + ('attrs', '23.2.0'), + ('lda', '3.0.0'), + ('gseapy', '0.10.8', { + 'checksums': ['15be80bac73768501f5cecf6751aeb2e41416fd144bd6daa2ec453ad08a10ce0'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('pybigtools', '0.1.2'), + ('pybiomart', '0.2.0', { + 'checksums': ['e9eac20db921820670c646d99725b0ee279e407379e5e8c3ec7245a07425d8fe'], + }), + ('pyranges', '0.0.111'), + ('pyrle', '0.0.39'), + ('pyvis', '0.3.2'), + ('requests_cache', '1.2.0'), + ('scanorama', '1.7.4'), + ('scatac_fragment_tools', '0.1.0'), + ('snakemake_interface_report_plugins', '1.0.0'), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('tmtoolkit', '0.12.0', { + # 'preinstallopts': local_tmtoolkit_preinstallkit, + 'checksums': ['6df5429cd675989f21d9f075ddb11fe5ae273d6544fc337a2589bab2bc331909'], + }), + ('tspex', '0.6.3', { + 'checksums': ['315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316'], + }), + ('typing', '3.7.4.3'), + ('pandoc', '2.3', { + 'checksums': ['e772c2c6d871146894579828dbaf1efd538eb64fc7e71d4a6b3a11a18baef90d'], + }), + ('nbsphinx', '0.9.4'), + ('nbsphinx-link', '1.3.0'), + ('numpydoc', '1.7.0'), + ('pyOpenSSL', '24.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['cabed4bfaa5df9f1a16c0ef64a0cb65318b5cd077a7eda7d6970131ca2f41a6f'], + }), + ('papermill', '2.6.0'), + ('loomxpy', '0.4.2', { + 'checksums': ['188411b77e04fa8458c0a7f02cfb3f15b58410a020f81f522957e922e79cdd82'], + }), + ('pycisTopic', '1.0.2', { + 'modulename': 'pycisTopic', + # 'patches': ['pycisTopic-1.0.2-manual_versioning.patch'], + # 'preinstallopts': local_pycistopic_preinstallopts, + 'source_urls': ['https://github.com/aertslab/pycisTopic/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + }), + ('pycistarget', '1.0.2', { + 'source_urls': ['https://github.com/aertslab/pycistarget/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + }), + (name, version, { + 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + 'sources': [ + { + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + } + ], + }), +] + + # (name, version, { + # 'source_urls': ['https://github.com/aertslab/scenicplus/archive/'], + # 'sources': [ + # { + # 'download_filename': '%s.tar.gz' % local_commit, + # 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit, + # } + # ], + # }), + +moduleclass = 'bio'