GNU bug report logs -
#60729
[PATCH] gnu: Add cellsnp-lite.
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Reported by: zimoun <zimon.toutoune <at> gmail.com>
Date: Wed, 11 Jan 2023 13:49:01 UTC
Severity: normal
Tags: patch
Done: Ricardo Wurmus <rekado <at> elephly.net>
Bug is archived. No further changes may be made.
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Report forwarded
to
rekado <at> elephly.net, guix-patches <at> gnu.org
:
bug#60729
; Package
guix-patches
.
(Wed, 11 Jan 2023 13:49:02 GMT)
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to
zimoun <zimon.toutoune <at> gmail.com>
:
New bug report received and forwarded. Copy sent to
rekado <at> elephly.net, guix-patches <at> gnu.org
.
(Wed, 11 Jan 2023 13:49:02 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Simon Tournier <zimon.toutoune <at> gmail.com>
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
---
gnu/packages/bioinformatics.scm | 44 ++++++++++++++++++++++++++++++++-
1 file changed, 43 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6e909773a7..4ef9ec15b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,7 +21,7 @@
;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki <at> gmail.com>
;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
-;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune <at> gmail.com>
+;;; Copyright © 2021, 2022, 2023 Simon Tournier <zimon.toutoune <at> gmail.com>
;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
;;; Copyright © 2022 Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
;;; Copyright © 2022 Antero Mejr <antero <at> mailbox.org>
@@ -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
Reply sent
to
Ricardo Wurmus <rekado <at> elephly.net>
:
You have taken responsibility.
(Thu, 12 Jan 2023 20:40:01 GMT)
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Notification sent
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zimoun <zimon.toutoune <at> gmail.com>
:
bug acknowledged by developer.
(Thu, 12 Jan 2023 20:40:01 GMT)
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Message #10 received at 60729-done <at> debbugs.gnu.org (full text, mbox):
zimoun <zimon.toutoune <at> gmail.com> writes:
> From: Simon Tournier <zimon.toutoune <at> gmail.com>
>
> * gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
Applied, thank you!
--
Ricardo
bug archived.
Request was from
Debbugs Internal Request <help-debbugs <at> gnu.org>
to
internal_control <at> debbugs.gnu.org
.
(Fri, 10 Feb 2023 12:24:05 GMT)
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This bug report was last modified 1 year and 76 days ago.
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