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01/01: gnu: Add kallisto.
From: |
Ricardo Wurmus |
Subject: |
01/01: gnu: Add kallisto. |
Date: |
Sun, 3 Dec 2017 12:39:06 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit d112e5a8c2cfc3ff32b143f5a92964e849631ca2
Author: Ricardo Wurmus <address@hidden>
Date: Fri Dec 1 10:52:55 2017 +0100
gnu: Add kallisto.
* gnu/packages/bioinformatics.scm (kallisto): New variable.
---
gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b3eec8..f0b589b 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)))