From efecefd4dd2483b350b496e0c192772dbc992f92 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Fri, 7 Jul 2017 20:15:38 -0700 Subject: Add a package for tophat (#4698) Lightly tested on CentOS 7. --- var/spack/repos/builtin/packages/tophat/package.py | 47 ++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/tophat/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py new file mode 100644 index 0000000000..116db56b32 --- /dev/null +++ b/var/spack/repos/builtin/packages/tophat/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 Tophat(AutotoolsPackage): + """Spliced read mapper for RNA-Seq.""" + + homepage = "http://ccb.jhu.edu/software/tophat/index.shtml" + url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz" + + version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + depends_on('boost@1.47:') + depends_on('bowtie2', type='run') + + parallel = False + + def configure_args(self): + return ["--with-boost={0}".format(self.spec['boost'].prefix)] -- cgit v1.2.3-70-g09d2