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mothur: new package (#5055)

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* mothur: new package

* fixing mpi things
This commit is contained in:
Audrey Thoma 2017-08-10 18:09:40 -05:00 committed by Adam J. Stewart
parent df3bc3906d
commit 518993431d
1 changed files with 59 additions and 0 deletions
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var/spack/repos/builtin/packages/mothur/package.py Normal file
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##############################################################################
# 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 Mothur(MakefilePackage):
"""This project seeks to develop a single piece of open-source, expandable
software to fill the bioinformatics needs of the microbial ecology
community."""
homepage = "https://github.com/mothur/mothur"
url = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz"
version('1.39.5', '1f826ea4420e6822fc0db002c5940b92')
variant('mpi', default=True, description='Enable MPI parallel support')
depends_on('mpi', when='+mpi')
depends_on('boost')
depends_on('readline')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
makefile.filter('BOOST_LIBRARY_DIR=\"\\\"Enter_your_boost_library_path'
'_here\\\"\"', 'BOOST_LIBRARY_DIR=%s' %
self.spec['boost'].prefix.lib)
makefile.filter('BOOST_INCLUDE_DIR=\"\\\"Enter_your_boost_include_path'
'_here\\\"\"', 'BOOST_INCLUDE_DIR=%s' %
self.spec['boost'].prefix.include)
makefile.filter('MOTHUR_FILES=\"\\\"Enter_your_default_path_'
'here\\\"\"', 'MOTHUR_FILES=%s' % prefix)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('mothur', prefix.bin)
install('uchime', prefix.bin)
install_tree('source', prefix.include)