Subject: [PATCH] gnu: Add python-baltica.
From: Navid Afkhami <[email-masked]>
To: <[email-masked]>
Cc: Navid Afkhami <[email-masked]>
Date: Tue, 1 Aug 2023 13:46:37 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

* 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