diff options
| author | Simon Tournier <zimon.toutoune@gmail.com> | 2023-01-11 14:47:44 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-01-12 21:37:56 +0100 |
| commit | 483bc044eb868f533c7e6923bb93398fcf04f9ba (patch) | |
| tree | 59da813b8db6b0111291491bcb9481f0898bc4f7 /gnu/packages/bioinformatics.scm | |
| parent | 98ef4ab23edb88e8dd09948f52f34fecbf9500f3 (diff) | |
gnu: Add cellsnp-lite.
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 44 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e909773a7..aff2f6dd9f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 @@ BED, GFF/GTF, VCF.") (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") |