From fa39afb59853b5971d9a70acbe50710da67ff2ac Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Fri, 18 Aug 2017 16:02:15 -0500 Subject: cufflinks: new package (#5158) --- .../repos/builtin/packages/cufflinks/package.py | 46 ++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cufflinks/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cufflinks/package.py b/var/spack/repos/builtin/packages/cufflinks/package.py new file mode 100644 index 0000000000..c0d331439b --- /dev/null +++ b/var/spack/repos/builtin/packages/cufflinks/package.py @@ -0,0 +1,46 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Cufflinks(Package): + """Cufflinks assembles transcripts, estimates their abundances, and tests + for differential expression and regulation in RNA-Seq samples.""" + + homepage = "http://cole-trapnell-lab.github.io/cufflinks" + url = "http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz" + + version('2.2.1', '7e693d182dcfda8aeef8523219ea9ea7') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('cuffcompare', prefix.bin) + install('cuffdiff', prefix.bin) + install('cufflinks', prefix.bin) + install('cuffmerge', prefix.bin) + install('cuffnorm', prefix.bin) + install('cuffquant', prefix.bin) + install('gffread', prefix.bin) + install('gtf_to_sam', prefix.bin) -- cgit v1.2.3-70-g09d2