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##############################################################################
# Copyright (c) 2013-2017, 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/spack/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 Mrbayes(AutotoolsPackage):
"""MrBayes is a program for Bayesian inference and model choice across a
wide range of phylogenetic and evolutionary models. MrBayes uses Markov
chain Monte Carlo (MCMC) methods to estimate the posterior distribution
of model parameters."""
homepage = "http://mrbayes.sourceforge.net"
url = "https://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz"
version('3.2.6', '95f9822f24be47b976bf87540b55d1fe')
variant('mpi', default=True, description='Enable MPI parallel support')
variant('beagle', default=True, description='Enable BEAGLE library for speed benefits')
variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
depends_on('autoconf', type='build')
depends_on('automake', type='build')
depends_on('libtool', type='build')
depends_on('m4', type='build')
depends_on('libbeagle', when='+beagle')
depends_on('mpi', when='+mpi')
configure_directory = 'src'
def configure_args(self):
args = []
if '~beagle' in self.spec:
args.append('--with-beagle=no')
else:
args.append('--with-beagle=%s' % self.spec['libbeagle'].prefix)
if '~sse' in self.spec:
args.append('--enable-sse=no')
else:
args.append('--enable-sse=yes')
if '~mpi' in self.spec:
args.append('--enable-mpi=no')
else:
args.append('--enable-mpi=yes')
return args
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('src'):
install('mb', prefix.bin)
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