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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 69 |
1 files changed, 69 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89f8041d56..e7c15f94c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1298,6 +1298,75 @@ pretty, publication-quality figures for next-generation sequencing experiments.") (license license:expat))) +(define-public python-cell2cell + (package + (name "python-cell2cell") + (version "0.6.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/earmingol/cell2cell") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hwww0rcv8sc4k312n4d0jhbyix1jjqgv5djg25bw8127q5iym3s")) + (modules '((guix build utils))) + (snippet + '(begin + ;; We remove the dependency on statannotations because it + ;; will not work with the current version of seaborn. See + ;; https://github.com/trevismd/statannotations/issues/122 + (substitute* "cell2cell/plotting/factor_plot.py" + (("from statannotations.Annotator import Annotator") + "") + (("if statistical_test is not None") + "if False")) + (substitute* "setup.py" + (("'statannotations',") "") + ;; We provide version 1.0.4, which should be fine. + (("'gseapy == 1.0.3'") "'gseapy'") + ;; Using matplotlib 3.5.2 leads to this bug: + ;; https://github.com/earmingol/cell2cell/issues/19 but we + ;; can't package a different minor version of matplotlib + ;; and limit its use to just this package. + (("matplotlib >= 3.2.0,<=3.5.1") "")))))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ;There are no tests + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs + (list python-gseapy + python-kneed + python-matplotlib + python-networkx + python-numpy + python-openpyxl + python-pandas + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-scanpy + python-seaborn + python-tensorly + python-tqdm + python-umap-learn + python-xlrd)) + (home-page "https://github.com/earmingol/cell2cell") + (synopsis "Python library for cell communication analysis") + (description + "Cell2cell is a Python library for cell communication analysis. +This is a method to calculate, visualize and analyze communication between +cell types. Cell2cell is suitable for single-cell RNA sequencing +(scRNA-seq) data.") + (license license:bsd-3))) + (define-public python-cellbender (package (name "python-cellbender") |