gnu: Add cellsnp-lite.

* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
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Simon Tournier 2023-01-11 14:47:44 +01:00 committed by Ricardo Wurmus
parent 98ef4ab23e
commit 483bc044eb
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@ -21,7 +21,7 @@
;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com>
;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2022 Navid Afkhami <navid.afkhami@mdc-berlin.de>
;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
@ -512,6 +512,49 @@ (define-public bedtools-2.18
(inputs
(list samtools zlib))))
(define-public cellsnp-lite
;; Last release is from November 2021 and does not contain fixes.
(let ((commit "0885d746b0b1ea65c8ef92f8943ca7669ca9734a")
(revision "0"))
(package
(name "cellsnp-lite")
(version (git-version "1.2.2" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/single-cell-genetics/cellsnp-lite")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1qrvqgbvw6mbhpyqvqbmvv8dmyc67bsk1041cn7ib6zmd47qm444"))))
(build-system gnu-build-system)
(arguments
(list
#:configure-flags
#~(list (string-append "--with-htslib="
#$(this-package-input "htslib")))))
(inputs
(list curl
htslib
openssl
zlib))
(native-inputs
(list autoconf))
(home-page "https://cellsnp-lite.readthedocs.io")
(synopsis "Pileup expresses alleles in single-cell or bulk RNA-seq data")
(description
"This package is designed to pileup the expressed alleles in
single-cell or bulk RNA-seq data, which can be directly used for donor
deconvolution in multiplexed single-cell RNA-seq data, particularly with other
packages, which assigns cells to donors and detects doublets as vireo, even
without genotyping reference.
This package is the C version of the deprecated cellSNP implemented in Python.
Compared to cellSNP, this package is more efficient with higher speed and less
memory usage.")
(license license:asl2.0))))
(define-public pbcopper
(package
(name "pbcopper")