[PATCH] gnu: Add kallisto.

DoneSubmitted by Ricardo Wurmus.
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  • Ricardo Wurmus
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Ricardo Wurmus wrote on 1 Dec 2017 13:31
(address . guix-patches@gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20171201123114.4262-1-rekado@elephly.net
* gnu/packages/bioinformatics.scm (kallisto): New variable.--- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+)
Toggle diff (39 lines)diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scmindex 5b3eec86d..f0b589b6c 100644--- a/gnu/packages/bioinformatics.scm+++ b/gnu/packages/bioinformatics.scm@@ -11079,3 +11079,32 @@ contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data.") ;; GPLv3 only (license license:gpl3)))++(define-public kallisto+ (package+ (name "kallisto")+ (version "0.43.1")+ (source (origin+ (method url-fetch)+ (uri (string-append "https://github.com/pachterlab/"+ "kallisto/archive/v" version ".tar.gz"))+ (file-name (string-append name "-" version ".tar.gz"))+ (sha256+ (base32+ "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))+ (build-system cmake-build-system)+ (arguments `(#:tests? #f)) ; no "check" target+ (inputs+ `(("hdf5" ,hdf5)+ ("zlib" ,zlib)))+ (home-page "http://pachterlab.github.io/kallisto/")+ (synopsis "Near-optimal RNA-Seq quantification")+ (description+ "Kallisto is a program for quantifying abundances of transcripts from+RNA-Seq data, or more generally of target sequences using high-throughput+sequencing reads. It is based on the novel idea of pseudoalignment for+rapidly determining the compatibility of reads with targets, without the need+for alignment. Pseudoalignment of reads preserves the key information needed+for quantification, and kallisto is therefore not only fast, but also as+accurate as existing quantification tools.")+ (license license:bsd-2)))-- 2.15.0
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Ricardo Wurmus wrote on 3 Dec 2017 23:17
control message for bug #29532
(address . control@debbugs.gnu.org)
E1eLcaQ-000309-2m@debbugs.gnu.org
tags 29532 fixedclose 29532
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