GNU bug report logs - #62989
[PATCH] gnu: Add python-rseqc.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
Subject: bug#62989: closed ([PATCH] gnu: Add python-rseqc.)
Date: Sat, 05 Aug 2023 21:30:02 +0000

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Your bug report

#62989: [PATCH] gnu: Add python-rseqc.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 62989 <at> debbugs.gnu.org.

-- 
62989: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=62989
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 62989-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-rseqc.
Date: Sat, 05 Aug 2023 23:27:23 +0200

I’m closing this because

1. we have a package for rseqc.
2. this is an unmaintained fork
3. IIRC it doesn’t actually work

-- 
Ricardo

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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-rseqc.
Date: Fri, 21 Apr 2023 10:28:45 +0000

* gnu/packages/bioinformatics.scm (python-rseqc): New variable.
---
 gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b27e12a5b4..ecc1815539 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3060,6 +3060,30 @@ (define-public python-pysam
 also includes an interface for tabix.")
     (license license:expat)))
 
+(define-public python-rseqc
+  (package
+    (name "python-rseqc")
+    (version "5.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "RSeQC" version))
+              (sha256
+               (base32
+                "106av4ms6agrfjdlw5j3fsrk86clr0f4ygysv19g66l6hj3laz9w"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-bx-python python-numpy python-pybigwig
+                             python-pysam))
+    (native-inputs (list python-cython python-nose))
+    (home-page "https://github.com/MonashBioinformaticsPlatform/RSeQC")
+    (synopsis "RNA-seq quality control packag")
+    (description
+     "Useful modules that can comprehensively evaluate high throughput sequence data.
+Some basic modules quickly inspect sequence, quality, nucleotide composition bias,
+PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation,
+mapped reads distribution, coverage uniformity, strand specificity, transcript level
+RNA integrity and etc.")
+    (license license:gpl3)))
+
 (define-public python-twobitreader
   (package
     (name "python-twobitreader")
-- 
2.34.1

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