From mboxrd@z Thu Jan 1 00:00:00 1970 From: Alex Vong Subject: Re: [PATCH] gnu: Add kallisto. Date: Wed, 18 Jan 2017 19:09:27 +0800 Message-ID: <87eg00mxp4.fsf@gmail.com> References: Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:49523) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTo7i-0006rF-2f for guix-devel@gnu.org; Wed, 18 Jan 2017 06:09:51 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTo7e-0007Cj-2H for guix-devel@gnu.org; Wed, 18 Jan 2017 06:09:50 -0500 Received: from mail-pg0-x241.google.com ([2607:f8b0:400e:c05::241]:34663) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cTo7d-0007Cd-Q5 for guix-devel@gnu.org; Wed, 18 Jan 2017 06:09:45 -0500 Received: by mail-pg0-x241.google.com with SMTP id t6so1163869pgt.1 for ; Wed, 18 Jan 2017 03:09:45 -0800 (PST) In-Reply-To: (Ra's message of "Wed, 18 Jan 2017 10:09:14 +0000") 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: Ra Cc: guix-devel --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello, Looking at the license text: Copyright =C2=A92015. The Regents of the University of California (Regents)= . All Rights Reserved. Permission to use, copy, modify, and distribute this softw= are and its documentation for educational and research not-for-profit purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following = two paragraphs appear in all copies, modifications, and distributions. Contact = The Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 51= 0, Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing opportunities. It seems the license is {fsf, dfsg} non-free because it does not allow commercial usage. More precisely, it violates freedom 0 (the freedom to run the program as you wish, for any purpose). Does anybody know of any fork or should we use an old version? Cheers, Alex Ra writes: > 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/bioinformatic= s.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 cleav= ages, > 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 r= apidly > +determining the compatibility of reads with targets, without the need fo= r alignment.") > + (license license:bsd-3))) > -- > 1.9.1 > > From f30c6b20e2564f3617ab3dde40af10bfbe790749 Mon Sep 17 00:00:00 2001 > From: Raoul Jean Pierre Bonnal > 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/bioinformatic= s.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 contain= s a number of utilities to > explore the MS/MS results and assess missed and irregular enzymatic clea= vages, > 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 fr= om > +RNA-Seq data, or more generally of target sequences using high-throughput > +sequencing reads. It is based on the novel idea of pseudoalignment for r= apidly > +determining the compatibility of reads with targets, without the need fo= r alignment.") > + (license license:bsd-3))) --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEdZDkzSn0Cycogr9IxYq4eRf1Ea4FAlh/TOcACgkQxYq4eRf1 Ea6q7A//cdd+TmdNGvVkkpvlkTKigVMgyRs0jX+wuRofKVmg4P3Kg5EUuE5tciCD nXQFNLPjpEIf1aROKtU7VIbzQ8D8vuMKX4hBxvSfk9AJj93RYOZ5HletJs2oj/Nz kwiSK6G/FN4y61QBb2e8/MSVqob4iegrIyJrrH0bcEUka0tvGxskYMZM3TDWqYMF 4tnO+zMe0uVt3ShnrhMFulO431Dpi/ni8h6cTFvaiPkEcFOLzM3zloDXWjQF6lw9 dK4Ueo6xXRWrbNER2thArTOWZbfLaA3ZHz4v4NN+rUFu3XbWQ2ISLTYvqWARM3iV 9IAI1VQZVy0KCrMBP0K8MXsCyzLVNgQ/fREw1q+2pjqpws863CWnKlZ0KNVclz5S ZYCbRq49A/pwAjVko6VtMcSmD/a95cWwz6/lbFViJnHeZKfG3cdDGgE8rhIMvWMt mG18iBu0U3bhvATW3zdyReImoEUe1Otvief+tQ18gE+9s1slwqrMylX27JLSP72s JSCcufLKnKo33Dic3DsmTgflEva1CGQ65s0DEozHrMjPDeDMNCoerVf9kwvq7cQW 469PzMlCKKmrmq63oYgMYeaMpq6/+Ok4yvEbMgRWbt1Mq6m4fEcZFttYqYVPltri 0sOBzcdLo4WYQYXCBA3wgwwHhQ7U5INrD+c7Y+9RjGZ/OY0cCdY= =4eQF -----END PGP SIGNATURE----- --=-=-=--