gnu: Add python-cmseq.
* gnu/packages/bioinformatics.scm (python-cmseq): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
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@ -11,7 +11,7 @@
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;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
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;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
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;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
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;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
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;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
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;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
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;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
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@ -1021,6 +1021,42 @@ Format (GFF) with Biopython integration.")
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from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
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from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
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(license license:bsd-3)))
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(license license:bsd-3)))
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(define-public python-cmseq
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(package
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(name "python-cmseq")
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(version "1.0.4")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "CMSeq" version))
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(sha256
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(base32
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"0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:tests? #false ;there are no tests
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#:phases
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'(modify-phases %standard-phases
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(add-after 'unpack 'patch-samtools-reference
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "cmseq/cmseq.py"
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(("'samtools'")
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(string-append "'" (search-input-file inputs "/bin/samtools") "'"))))))))
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(inputs (list samtools))
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(propagated-inputs
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(list python-bcbio-gff/biopython-1.73
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python-biopython-1.73
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python-numpy
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python-pandas
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python-pysam
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python-scipy))
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(home-page "https://github.com/SegataLab/cmseq/")
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(synopsis "Set of utilities on sequences and BAM files")
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(description
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"CMSeq is a set of commands to provide an interface to .bam files for coverage
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and sequence consensus.")
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(license license:expat)))
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(define-public python-htsget
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(define-public python-htsget
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(package
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(package
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(name "python-htsget")
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(name "python-htsget")
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