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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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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