Navid Afkhami wrote 2 years ago
(address . guix-patches@gnu.org)(name . Navid Afkhami)(address . navid.afkhami@mdc-berlin.de)
13266f60b98b4632c6b7fa2c4e5cacdc3a0840f7.1685719423.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.
---
gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++
1 file changed, 64 insertions(+)
Toggle diff (79 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 89f8041d56..6dbbc26eac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1298,6 +1298,70 @@ (define-public python-biofluff
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
+ (substitute* "cell2cell/plotting/factor_plot.py"
+ (("from statannotations.Annotator import Annotator")
+ "")
+ (("if statistical_test is not None")
+ "if False"))
+ (substitute* "setup.py"
+ (("'statannotations',")
+ ""))
+ (substitute* "setup.py"
+ (("matplotlib >= 3.2.0,<=3.5.1")
+ ""))
+ (substitute* "setup.py"
+ (("'gseapy == 1.0.3'")
+ "'gseapy'"))))))
+ (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))
+ (native-inputs (list python-pytest))
+ (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")
base-commit: a7d9cd742c3149bb014db95f88d1158d590bc124
--
2.34.1