Navid Afkhami wrote 2 years ago
(address . guix-patches@gnu.org)
f9425fb2ae20749a606fbde79e278fd9f643767e.1690108906.git.navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-liana-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 864c200707..a0ae298a2c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1863,6 +1863,64 @@ (define-public python-htsget
servers supporting the protocol.")
(license license:asl2.0)))
+(define-public python-liana-py
+ (package
+ (name "python-liana-py")
+ (version "0.1.9")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/saezlab/liana-py")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "00lqrmi38wmdpjlcafgmrnkwsbp0yvm2rya6qs8y6jfizww9ff8i"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:test-flags '(list "-k"
+ ;; These tests require internet access.
+ (string-append "not test_generate_lr_resource"
+ " and not test_generate_nondefault_lr_resource"))
+ #:phases '(modify-phases %standard-phases
+ (add-before 'check 'set-home
+ ;; Some tests require home directory to be set.
+ (lambda _
+ (setenv "HOME" "/tmp")))
+ ;; Numba needs a writable directory to cache functions.
+ (add-before 'build 'set-numba-cache-dir
+ (lambda _
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (propagated-inputs (list python-anndata
+ python-black
+ python-cell2cell
+ python-decoupler-py
+ python-hypothesis
+ python-ipykernel
+ python-ipython
+ python-mofax
+ python-mudata
+ python-nbconvert
+ python-nbsphinx
+ python-numpydoc
+ python-omnipath
+ python-pandas
+ python-plotnine
+ python-pypandoc
+ python-scipy
+ python-requests
+ python-scanpy
+ python-statsmodels
+ python-tqdm
+ tzdata))
+ (native-inputs (list python-pytest python-pytest-cov python-numpy))
+ (home-page "https://github.com/saezlab/liana-py")
+ (synopsis "LIANA is a ligand-receptor analysis framework")
+ (description "This is a Ligand-Receptor inference framework.
+The framework enables the use of any LR method
+with any resources.")
+ (license license:gpl3+)))
+
(define-public python-logomaker
(package
(name "python-logomaker")
base-commit: 445a0359083388b5ee686e6e855f94a3aac5f79c
--
2.34.1