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new 483bc044eb gnu: Add cellsnp-lite.
483bc044eb is described below
commit 483bc044eb868f533c7e6923bb93398fcf04f9ba
Author: Simon Tournier <[email protected]>
AuthorDate: Wed Jan 11 14:47:44 2023 +0100
gnu: Add cellsnp-lite.
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
---
gnu/packages/bioinformatics.scm | 45 ++++++++++++++++++++++++++++++++++++++++-
1 file changed, 44 insertions(+), 1 deletion(-)
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 <[email protected]>
;;; Copyright © 2021 Tim Howes <[email protected]>
;;; Copyright © 2021 Hong Li <[email protected]>
-;;; Copyright © 2021, 2022 Simon Tournier <[email protected]>
+;;; Copyright © 2021, 2022, 2023 Simon Tournier <[email protected]>
;;; Copyright © 2021 Felix Gruber <[email protected]>
;;; Copyright © 2022 Navid Afkhami <[email protected]>
;;; Copyright © 2022 Antero Mejr <[email protected]>
@@ -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")
