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gnu: Add python-cmseq.

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* gnu/packages/bioinformatics.scm (python-cmseq): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
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Mădălin Ionel Patrașcu 2023-01-22 01:49:48 +01:00 committed by Ricardo Wurmus
parent 9558da5bb4
commit 47839a9ed6
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1 changed files with 37 additions and 1 deletions
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38
gnu/packages/bioinformatics.scm
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@ -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 @@ (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 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")