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04/06: gnu: Add python-cmseq.
From: |
guix-commits |
Subject: |
04/06: gnu: Add python-cmseq. |
Date: |
Tue, 24 Jan 2023 18:23:51 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 47839a9ed662f67941bae41a507903280c4f06fd
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Sun Jan 22 01:49:48 2023 +0100
gnu: Add python-cmseq.
* gnu/packages/bioinformatics.scm (python-cmseq): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
---
gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++++++-
1 file changed, 37 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index da65fcb92f..a52a36bdac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11,7 +11,7 @@
;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu
<madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu
<madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
@@ -1021,6 +1021,42 @@ Format (GFF) with Biopython integration.")
from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
(license license:bsd-3)))
+(define-public python-cmseq
+ (package
+ (name "python-cmseq")
+ (version "1.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "CMSeq" version))
+ (sha256
+ (base32
+ "0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are no tests
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'patch-samtools-reference
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "cmseq/cmseq.py"
+ (("'samtools'")
+ (string-append "'" (search-input-file inputs "/bin/samtools")
"'"))))))))
+ (inputs (list samtools))
+ (propagated-inputs
+ (list python-bcbio-gff/biopython-1.73
+ python-biopython-1.73
+ python-numpy
+ python-pandas
+ python-pysam
+ python-scipy))
+ (home-page "https://github.com/SegataLab/cmseq/")
+ (synopsis "Set of utilities on sequences and BAM files")
+ (description
+ "CMSeq is a set of commands to provide an interface to .bam files for
coverage
+and sequence consensus.")
+ (license license:expat)))
+
(define-public python-htsget
(package
(name "python-htsget")
- branch master updated (f9c151b936 -> 718223c58c), guix-commits, 2023/01/24
- 04/06: gnu: Add python-cmseq.,
guix-commits <=
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