[PATCH] gnu: Add kallisto.

[Ra <ilpuccio.febo@gmail.com>]

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Hi,
I think I need your help to identify the right license for this package, I
set bsd-3 only for convenience this is the original license (
https://github.com/pachterlab/kallisto/blob/master/license.txt)

Do I need to use something like :

(license (license:non-copyleft "file://src/COPYING"
                                   "See src/COPYING in the distribution."))))




* gnu/packages/bioinformatics.scm (kallisto): New variable.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index c60bedc..86026fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8502,3 +8502,31 @@ a specified false discovery rate.  It also contains
a number of utilities to
 explore the MS/MS results and assess missed and irregular enzymatic
cleavages,
 mass measurement accuracy, etc.")
     (license license:artistic2.0)))
+
+(define-public kallisto
+  (package
+    (name "kallisto")
+    (version "0.43.0")
+    (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
+                "1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f)) ; no "check" target
+    (inputs
+     `(("zlib" ,zlib)
+       ("hdf5" ,hdf5)))
+    (home-page "https://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.")
+    (license license:bsd-3)))
--
1.9.1

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From f30c6b20e2564f3617ab3dde40af10bfbe790749 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Wed, 18 Jan 2017 10:46:49 +0100
Subject: [PATCH] gnu: Add kallisto.

* gnu/packages/bioinformatics.scm (kallisto): New variable.
---
 gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c60bedc..86026fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8502,3 +8502,31 @@ a specified false discovery rate.  It also contains a number of utilities to
 explore the MS/MS results and assess missed and irregular enzymatic cleavages,
 mass measurement accuracy, etc.")
     (license license:artistic2.0)))
+
+(define-public kallisto
+  (package
+    (name "kallisto")
+    (version "0.43.0")
+    (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
+                "1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrhcnrb2davhv9"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f)) ; no "check" target
+    (inputs
+     `(("zlib" ,zlib)
+       ("hdf5" ,hdf5)))
+    (home-page "https://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.")
+    (license license:bsd-3)))
-- 
1.9.1