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##############################################################################
# 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/spack/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)
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