* [bug#64992] [PATCH] gnu: Add python-baltica.
@ 2023-08-01 13:46 Navid Afkhami
2023-08-02 6:48 ` bug#64992: " Ricardo Wurmus
0 siblings, 1 reply; 2+ messages in thread
From: Navid Afkhami @ 2023-08-01 13:46 UTC (permalink / raw)
To: 64992; +Cc: Navid Afkhami
* gnu/packages/bioinformatics.scm (python-baltica): New variable.
---
gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6080c899af..6d745262b3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5056,6 +5056,49 @@ (define-public edirect-go-programs
go-golang-org-x-image
go-golang-org-x-text))))
+(define-public python-baltica
+ (package
+ (name "python-baltica")
+ (version "1.1.2")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dieterich-lab/Baltica")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:phases '(modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ ;; The tests need to be run from elsewhere...
+ (mkdir-p "/tmp/test")
+ (copy-recursively ".tests" "/tmp/test")
+ (with-directory-excursion "/tmp/test"
+ (invoke "pytest" "-v" "--doctest-modules")))))))
+ (propagated-inputs (list python-anndata
+ python-click
+ python-flask
+ python-flask-wtf
+ gunicorn
+ python-h5py
+ python-pysam
+ python-numpy
+ python-psutil
+ python-pyyaml
+ python-scipy
+ snakemake-7))
+ (native-inputs (list python-pytest python-pyfakefs python-cython))
+ (home-page "https://github.com/dieterich-lab/Baltica")
+ (synopsis "Integrated splice junction usage analysis")
+ (description
+ "This framework facilitates the execution of differential junction usage methods.
+Additionally, it enables the integration of results from multiple DJU methods.")
+ (license license:expat)))
+
(define-public python-bamnostic
(package
(name "python-bamnostic")
base-commit: 34b56974dfe720e5e30f04409ac216747d7e3f5c
--
2.34.1
^ permalink raw reply related [flat|nested] 2+ messages in thread
* bug#64992: [PATCH] gnu: Add python-baltica.
2023-08-01 13:46 [bug#64992] [PATCH] gnu: Add python-baltica Navid Afkhami
@ 2023-08-02 6:48 ` Ricardo Wurmus
0 siblings, 0 replies; 2+ messages in thread
From: Ricardo Wurmus @ 2023-08-02 6:48 UTC (permalink / raw)
To: 64992-done
Pushed with commit 5a293d0830aa9369e388d37fe767d5bf98af01b7. Thanks for
the patch!
--
Ricardo
^ permalink raw reply [flat|nested] 2+ messages in thread
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2023-08-01 13:46 [bug#64992] [PATCH] gnu: Add python-baltica Navid Afkhami
2023-08-02 6:48 ` bug#64992: " Ricardo Wurmus
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