##############################################################################
# Copyright (c) 2013-2016, 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/llnl/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 *


class Hmmer(Package):
    """HMMER is used for searching sequence databases for sequence homologs,
    and for making sequence alignments. It implements methods using
    probabilistic models called profile hidden Markov models (profile HMMs).
    """
    homepage = 'http://www.hmmer.org'
    url      = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'

    version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
    version('3.0',   '4cf685f3bc524ba5b5cdaaa070a83588')
    version('2.4i',  'dab234c87e026ac1de942450750acd20')
    version('2.3.2', '5f073340c0cf761288f961a73821228a')
    version('2.3.1', 'c724413e5761c630892506698a4716e2')

    variant('mpi', default=True,  description='Compile with MPI')
    variant('gsl', default=False, description='Compile with GSL')

    depends_on('mpi', when='+mpi')
    depends_on('gsl', when='+gsl')

    def url_for_version(self, version):
        base_url = 'http://eddylab.org/software'

        if version >= Version('3.0'):
            return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
        else:
            return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)

    def install(self, spec, prefix):
        configure_args = [
            '--prefix={0}'.format(prefix)
        ]

        if '+gsl' in self.spec:
            configure_args.extend([
                '--with-gsl',
                'LIBS=-lgsl -lgslcblas'
            ])

        if '+mpi' in self.spec:
            configure_args.append('--enable-mpi')

        configure(*configure_args)
        make()

        if self.run_tests:
            make('check')

        make('install')