77 lines
2.8 KiB
Python
77 lines
2.8 KiB
Python
##############################################################################
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# Copyright (c) 2013-2016, 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/llnl/spack
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# Please also see the LICENSE file 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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class Hmmer(Package):
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"""HMMER is used for searching sequence databases for sequence homologs,
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and for making sequence alignments. It implements methods using
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probabilistic models called profile hidden Markov models (profile HMMs).
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"""
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homepage = 'http://www.hmmer.org'
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url = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
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version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
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version('3.0', '4cf685f3bc524ba5b5cdaaa070a83588')
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version('2.4i', 'dab234c87e026ac1de942450750acd20')
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version('2.3.2', '5f073340c0cf761288f961a73821228a')
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version('2.3.1', 'c724413e5761c630892506698a4716e2')
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variant('mpi', default=True, description='Compile with MPI')
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variant('gsl', default=False, description='Compile with GSL')
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depends_on('mpi', when='+mpi')
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depends_on('gsl', when='+gsl')
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def url_for_version(self, version):
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base_url = 'http://eddylab.org/software'
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if version >= Version('3.0'):
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return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
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else:
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return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
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def install(self, spec, prefix):
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configure_args = [
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'--prefix={0}'.format(prefix)
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]
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if '+gsl' in self.spec:
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configure_args.extend([
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'--with-gsl',
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'LIBS=-lgsl -lgslcblas'
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])
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if '+mpi' in self.spec:
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configure_args.append('--enable-mpi')
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configure(*configure_args)
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make()
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if self.run_tests:
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make('check')
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make('install')
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