From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ra Subject: [PATCH] gnu: Add kallisto. Date: Wed, 18 Jan 2017 10:09:14 +0000 Message-ID: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary=94eb2c05d5107dfc3905465b9cd0 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36329) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTnBJ-0005WI-7i for guix-devel@gnu.org; Wed, 18 Jan 2017 05:09:30 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTnBH-0000MI-RJ for guix-devel@gnu.org; Wed, 18 Jan 2017 05:09:29 -0500 Received: from mail-qk0-x230.google.com ([2607:f8b0:400d:c09::230]:36443) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cTnBH-0000Kz-KV for guix-devel@gnu.org; Wed, 18 Jan 2017 05:09:27 -0500 Received: by mail-qk0-x230.google.com with SMTP id 11so7985142qkl.3 for ; Wed, 18 Jan 2017 02:09:26 -0800 (PST) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel --94eb2c05d5107dfc3905465b9cd0 Content-Type: multipart/alternative; boundary=94eb2c05d5107dfc3405465b9cce --94eb2c05d5107dfc3405465b9cce Content-Type: text/plain; charset=UTF-8 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 --94eb2c05d5107dfc3405465b9cce Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi,
I think I need your help to identify th= e right license for this package, I set bsd-3 only for convenience this is = the original license (https://github.com/pachterlab/kallisto/blob/master/li= cense.txt)

Do I need to use something like :
(license (license:non-copyleft "file://src/COPYING=
"
                                   "See src/COPYING in the distributio=
n."))))



* gnu/packages/bioinformatics.scm (kallisto): New variable.
=
---
=C2=A0gnu/packages/bioinformatics.scm | 28 +++++++++++++= +++++++++++++++
=C2=A01 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.=C2= =A0 It also contains a number of utilities to
=C2=A0explore the M= S/MS results and assess missed and irregular enzymatic cleavages,
=C2=A0mass measurement accuracy, etc.")
=C2=A0 =C2=A0 =C2= =A0(license license:artistic2.0)))
+
+(define-public ka= llisto
+ =C2=A0(package
+ =C2=A0 =C2=A0(name "kall= isto")
+ =C2=A0 =C2=A0(version "0.43.0")
+ =C2=A0 =C2=A0(source (origin
+ =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0(method url-fetch)
+ =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0(uri (string-append
+ =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0"https://github.com/pachterlab/kalli= sto/archive/v"
+ =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0version ".tar.gz"))
+ = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(file-name (string-append n= ame "-" version ".tar.gz"))
+ =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0(sha256
+ =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 (base32
+ =C2=A0 =C2=A0 =C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0"1d9cqf3lz6mm9kmqn47d99c6byn6q9l4ppgcafxrh= cnrb2davhv9"))))
+ =C2=A0 =C2=A0(build-system cmake-build-sy= stem)
+ =C2=A0 =C2=A0(arguments
+ =C2=A0 =C2=A0 '(#= :tests? #f)) ; no "check" target
+ =C2=A0 =C2=A0(inputs=
+ =C2=A0 =C2=A0 `(("zlib" ,zlib)
+ =C2=A0 = =C2=A0 =C2=A0 ("hdf5" ,hdf5)))
+ =C2=A0 =C2=A0(home-pag= e "https://pachterla= b.github.io/kallisto")
+ =C2=A0 =C2=A0(synopsis "Ne= ar-optimal RNA-Seq quantification")
+ =C2=A0 =C2=A0(descript= ion
+ =C2=A0 =C2=A0 "Kallisto is a program for quantifying a= bundances 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
+determini= ng the compatibility of reads with targets, without the need for alignment.= ")
+ =C2=A0 =C2=A0(license license:bsd-3)))
--
1.9.1
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