63 lines
2.3 KiB
Python
63 lines
2.3 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import glob
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class SnapKorf(MakefilePackage):
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"""SNAP is a general purpose gene finding program suitable for both
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eukaryotic and prokaryotic genomes."""
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homepage = "http://korflab.ucdavis.edu/software.html"
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url = "http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz"
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version('2013-11-29', 'dfdf48e37cdb32af4eecd9201506b6e3')
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depends_on('perl', type=('build', 'run'))
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depends_on('boost')
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depends_on('sqlite')
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depends_on('sparsehash')
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conflicts('%gcc@5:', when='@2013-11-29')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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progs = ['snap', 'fathom', 'forge', 'depend', 'exonpairs', 'hmm-info']
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for p in progs:
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install(p, prefix.bin)
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files = glob.iglob('*.pl')
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for file in files:
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install(file, prefix.bin)
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install_tree('Zoe', prefix.Zoe)
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install_tree('HMM', prefix.HMM)
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install_tree('DNA', prefix.DNA)
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def setup_environment(self, spack_env, run_env):
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run_env.set('ZOE', self.prefix)
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run_env.prepend_path('PATH', self.prefix)
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