diff options
| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-01-22 01:49:48 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-01-25 00:22:53 +0100 |
| commit | 47839a9ed662f67941bae41a507903280c4f06fd (patch) | |
| tree | 8b9c7dc978f3f7aee4e5dedd15107ec8816d1b88 /gnu/packages/bioinformatics.scm | |
| parent | 9558da5bb484ae35e2a0da2390798cd2d1f23da0 (diff) | |
gnu: Add python-cmseq.
* gnu/packages/bioinformatics.scm (python-cmseq): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 |
1 files changed, 37 insertions, 1 deletions
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") |