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| author | Navid Afkhami <navid.afkhami@mdc-berlin.de> | 2023-06-05 17:05:35 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-06-05 17:11:15 +0200 |
| commit | 6559adea29ae116f5fa882f88678e510001e2c88 (patch) | |
| tree | c0992b01455f5907b5158109ebcde4a3fad2e69d | |
| parent | 91e75bb35fd545dc3dc5275428ca4cc17123c76c (diff) | |
| download | guix-6559adea29ae116f5fa882f88678e510001e2c88.tar.gz guix-6559adea29ae116f5fa882f88678e510001e2c88.zip | |
gnu: Add python-bulkvis.
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 251e46061f..5667fba689 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1337,6 +1337,74 @@ pretty, publication-quality figures for next-generation sequencing experiments.") (license license:expat))) +(define-public python-bulkvis + (let ((commit "00a82a90c7e748a34af896e779d27e78a2c82b5e") + (revision "2")) + (package + (name "python-bulkvis") + (version (git-version "2.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/LooseLab/bulkVis") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02blai158xyyqcg0ljzkmfa6ci05m4awrl4njvp9nwfp717xq8n0")) + (modules '((guix build utils))) + (snippet + '(substitute* '("requirements.txt" + "setup.py") + (("tqdm~=4.46.1") "tqdm") + (("tornado~=6.0.4") "tornado") + (("pandas~=1.0.5") "pandas") + (("h5py~=2.10.0") "h5py") + ;; See below for com + (("bokeh~=2.1.0") "bokeh"))))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;There are no tests + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'bokeh-compatibility + (lambda _ + (substitute* "bulkvis/bulkvis.py" + (("import importlib" m) + (string-append m " +from bokeh.command.subcommand import Argument +from bokeh.util.dataclasses import entries\n")) + (("( *)_parser.add_argument" m indent) + (string-append + (string-join (list "if isinstance(opts, Argument):\n" + " opts = dict(entries(opts))\n") + indent 'prefix) + m)))))))) + (propagated-inputs (list python-bokeh + python-dill + python-h5py + python-joblib + python-matplotlib + python-numpy + python-pandas + python-plotly + python-readpaf + python-scikit-learn + python-scikit-image + python-scipy + python-seaborn + python-tornado-6 + python-tqdm + python-umap-learn)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/LooseLab/bulkVis") + (synopsis "Interactive visualization of bulk RNA-seq data") + (description + "This is a Python package for the interactive visualization of bulk +RNA-seq data. It provides a range of plotting functions and interactive tools +to explore and analyze bulk RNA-seq data.") + (license license:expat)))) + (define-public python-cell2cell (package (name "python-cell2cell") |