Navid Afkhami wrote 2 years ago
(address . guix-patches@gnu.org)(name . Navid Afkhami)(address . navid.afkhami@mdc-berlin.de)
a1a2b8c0f38f7eab2d862ea37004531c04f5e74a.1686068146.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable.
---
gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
Toggle diff (73 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 509dc3358b..12455984ed 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1549,6 +1549,64 @@ (define-public python-cmseq
and sequence consensus.")
(license license:expat)))
+(define-public python-decoupler-py
+ ;; This latest commit fixes the bug in test_omnip.py file. check_if_omnipath() has changed to _check_if_omnipath()
+ (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f")
+ (revision "1"))
+ (package
+ (name "python-decoupler-py")
+ (version (git-version "1.3.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/saezlab/decoupler-py")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags '(list "-k"
+ ;; These tests require internet access
+ (string-append "not test_get_resource"
+ " and not test_show_resources"
+ " and not test_get_dorothea"
+ " and not test_get_progeny"
+ " and not test_plot_volcano"))
+ #:phases '(modify-phases %standard-phases
+ (add-before 'check 'set-home
+ ;; Some tests require a home directory to be set.
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ ;; 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-adjusttext
+ python-anndata
+ python-ipython
+ python-matplotlib
+ python-nbsphinx
+ python-numba
+ python-numpy
+ python-numpydoc
+ python-omnipath
+ python-scanpy
+ python-scikit-learn
+ python-scipy
+ python-skranger
+ python-tqdm
+ python-typing-extensions))
+ (native-inputs (list python-pytest))
+ (home-page "https://github.com/saezlab/decoupler-py")
+ (synopsis
+ "Framework for modeling, analyzing and interpreting single-cell RNA-seq data")
+ (description
+ "Different statistical methods to extract biological activities
+from omics data within a unified framework.")
+ (license license:gpl3+))))
+
(define-public python-demuxem
(package
(name "python-demuxem")
base-commit: 9ad8b0c2ef10d8de01bad25f54337c5df35aa842
--
2.34.1