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Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Hong Li -;;; Copyright © 2021, 2022 Simon Tournier +;;; Copyright © 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2021 Felix Gruber ;;; Copyright © 2022 Navid Afkhami ;;; Copyright © 2022 Antero Mejr @@ -512,6 +512,48 @@ (define-public bedtools-2.18 (inputs (list samtools zlib)))) +(define-public cellsnp-lite + ;; Last release 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. +Comparedto cellSNP, this package is more efficient with higher speed and less +memory usage.") + (license license:asl2.0)))) + (define-public pbcopper (package (name "pbcopper") base-commit: a8b2decf287498eeb51ef23712c5bd01b60cb18b -- 2.38.1