GNU bug report logs - #65364
[PATCH] gnu: Add python-scDamAndTools.

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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-scDamAndTools.
Date: Fri, 18 Aug 2023 14:01:06 +0000

* gnu/packages/bioinformatics.scm (python-scDamAndTools): New variable.
---
 gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 51640b710f..03b1e81634 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2154,6 +2154,40 @@ (define-public python-pybedtools
     ;; licensed lgpl2.1+
     (license (list license:expat license:lgpl2.1+))))
 
+(define-public python-scDamAndTools
+  (package
+    (name "python-scDamAndTools")
+    (version "1.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/KindLab/scDamAndTools")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1mblw6cn5jqik6ky8cv7ry99z6jm1i4r71pzdfl398vrwbda65gd"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ;there are none
+    (propagated-inputs (list python-h5py
+                             python-numpy
+                             python-sortedcontainers
+                             python-pandas
+                             python-pysam
+                             python-tqdm))
+    (native-inputs (list python-cython python-pytest))
+    (home-page "https://github.com/KindLab/scDamAndTools")
+    (synopsis "Functions for processing raw scDam&T-seq data")
+    (description
+     "This is a set of unctions for processing raw scDam&T-seq data.
+A method to simultaneously measure protein-DNA interactions and transcription
+from single cells (Rooijers et al., 2019). scDam&T-seq combines a DamID-based
+method to measure protein-DNA interactions and an adaptation of CEL-Seq to
+measure transcription.  The starting point of the workflow is raw sequencing
+data and the end result are tables of UMI-unique DamID and CEL-Seq counts.")
+    (license license:expat)))
+
 (define-public python-bioframe
   (package
     (name "python-bioframe")

base-commit: 1b2d43fe016848ea2ec16ff18cbc14340944fc4e
-- 
2.34.1

Message #10 received at 65364-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 65364-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-scDamAndTools.
Date: Mon, 28 Aug 2023 09:51:53 +0200

Thanks for the patch.  I renamed it to all lowercase and changed the
description a little bit.

Pushed!

-- 
Ricardo

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