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