From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <60997@debbugs.gnu.org>
Cc: rekado@elephly.net
Subject: [bug#60997] [PATCH 1/4] gnu: Add python-cmseq.
Date: Sun, 22 Jan 2023 01:49:48 +0100 [thread overview]
Message-ID: <20230122004951.119277-1-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <55c300694f6c49f6a89a8018a3f86729@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (python-cmseq): New variable.
---
gnu/packages/bioinformatics.scm | 29 ++++++++++++++++++++++++++++-
1 file changed, 28 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 36c9db90bd..4e7bc07a5f 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>
@@ -1014,6 +1014,33 @@ (define-public python-cellbender
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 python-build-system)
+ (arguments
+ (list #:tests? #f )) ;pypi no tests
+ (propagated-inputs
+ (list python-bcbio-gff
+ python-biopython
+ python-numpy
+ python-pandas
+ python-pysam
+ python-scipy))
+ (home-page "http://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")
base-commit: f088763356e88c4911ee933fdafcad6ed66a7aa3
--
2.39.1
next prev parent reply other threads:[~2023-01-22 0:51 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2023-01-22 0:44 [bug#60997] [patch] gnu: Add python-cmseq, python-cmseq, python-phylophlan and python-metaphlan MadalinIonel.Patrascu
2023-01-22 0:49 ` Mădălin Ionel Patrașcu [this message]
2023-01-22 0:49 ` [bug#60997] [PATCH 2/4] gnu: Add python-hclust2 Mădălin Ionel Patrașcu
2023-01-22 0:49 ` [bug#60997] [PATCH 3/4] gnu: Add python-phylophlan Mădălin Ionel Patrașcu
2023-01-24 9:10 ` Ricardo Wurmus
2023-01-22 0:49 ` [bug#60997] [PATCH 4/4] gnu: Add python-metaphlan Mădălin Ionel Patrașcu
2023-01-24 9:11 ` Ricardo Wurmus
2023-01-24 8:36 ` [bug#60997] [PATCH 1/4] gnu: Add python-cmseq Ricardo Wurmus
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