stacks: new package (#4875)

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Audrey Thoma 2017-07-24 19:50:40 -05:00 committed by Adam J. Stewart
parent 07e60bc26b
commit 4237e5fffd

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@ -0,0 +1,48 @@
##############################################################################
# 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 Stacks(AutotoolsPackage):
"""Stacks is a software pipeline for building loci from short-read
sequences, such as those generated on the Illumina platform."""
homepage = "http://catchenlab.life.illinois.edu/stacks/"
url = "http://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz"
version('1.46', '18b0568a4bba44fb4e5be0eb7ee2c08d')
variant('sparsehash', default=True, description='Improve Stacks memory usage with SparseHash')
depends_on('perl', type=('build', 'run'))
depends_on('sparsehash', when='+sparsehash')
def configure_args(self):
args = []
if '+sparsehash' in self.spec:
args.append('--enable-sparsehash')
else:
args.append('--disable-sparsehash')
return args