GNU bug report logs - #64992
[PATCH] gnu: Add python-baltica.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 64992 in the body.
You can then email your comments to 64992 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add python-baltica.
Date: Tue, 1 Aug 2023 13:46:37 +0000

* 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

Message #10 received at 64992-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 64992-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-baltica.
Date: Wed, 02 Aug 2023 08:48:37 +0200

Pushed with commit 5a293d0830aa9369e388d37fe767d5bf98af01b7.  Thanks for
the patch!

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.