From e3053d7425e10180a8a7d0521b89bdf710f87dc2 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 10 Oct 2017 13:09:31 -0500 Subject: snap-korf: new package (#5589) --- .../repos/builtin/packages/snap-korf/package.py | 62 ++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 var/spack/repos/builtin/packages/snap-korf/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/snap-korf/package.py b/var/spack/repos/builtin/packages/snap-korf/package.py new file mode 100644 index 0000000000..95191b1bd4 --- /dev/null +++ b/var/spack/repos/builtin/packages/snap-korf/package.py @@ -0,0 +1,62 @@ +############################################################################## +# Copyright (c) 2013-2017, 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 * +import glob + + +class SnapKorf(MakefilePackage): + """SNAP is a general purpose gene finding program suitable for both + eukaryotic and prokaryotic genomes.""" + + homepage = "http://korflab.ucdavis.edu/software.html" + url = "http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz" + + version('2013-11-29', 'dfdf48e37cdb32af4eecd9201506b6e3') + + depends_on('perl', type=('build', 'run')) + depends_on('boost') + depends_on('sqlite') + depends_on('sparsehash') + + conflicts('%gcc@5:', when='@2013-11-29') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + + progs = ['snap', 'fathom', 'forge', 'depend', 'exonpairs', 'hmm-info'] + for p in progs: + install(p, prefix.bin) + + files = glob.iglob('*.pl') + for file in files: + install(file, prefix.bin) + + install_tree('Zoe', prefix.Zoe) + install_tree('HMM', prefix.HMM) + install_tree('DNA', prefix.DNA) + + def setup_environment(self, spack_env, run_env): + run_env.set('ZOE', self.prefix) + run_env.prepend_path('PATH', self.prefix) -- cgit v1.2.3-60-g2f50