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# Copyright 2013-2022 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)
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"
git = "https://github.com/KorfLab/SNAP.git"
version('2021-11-04', commit='62ff3120fceccb03b5eea9d21afec3167dedfa94')
version('2013-11-29', sha256='e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a')
depends_on('perl', type=('build', 'run'))
def edit(self, spec, prefix):
if spec.satisfies('@2013-11-29%gcc@6:'):
rstr = '\\1 -Wno-tautological-compare -Wno-misleading-indentation'
filter_file('(-Werror)', rstr, 'Zoe/Makefile')
rstr = '\\1 -Wno-error=format-overflow -Wno-misleading-indentation'
filter_file('(-Werror)', rstr, 'Makefile')
filter_file(r'(^const char \* zoeFunction;)', 'extern \\1',
'Zoe/zoeTools.h')
filter_file(r'(^const char \* zoeConstructor;)', 'extern \\1',
'Zoe/zoeTools.h')
filter_file(r'(^const char \* zoeMethod;)', 'extern \\1',
'Zoe/zoeTools.h')
def install(self, spec, prefix):
mkdirp(prefix.bin)
progs = ['snap', 'fathom', 'forge']
if spec.satisfies('@2013-11-29'):
progs = progs + ['depend', 'exonpairs', 'hmm-info']
for p in progs:
install(p, prefix.bin)
install('*.pl', prefix.bin)
install_tree('Zoe', prefix.Zoe)
install_tree('HMM', prefix.HMM)
install_tree('DNA', prefix.DNA)
def setup_run_environment(self, env):
env.set('ZOE', self.prefix)
env.prepend_path('PATH', self.prefix)
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