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##############################################################################
# Copyright (c) 2013-2018, 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 Plink(Package):
"""PLINK is a free, open-source whole genome association analysis toolset,
designed to perform a range of basic, large-scale analyses in a
computationally efficient manner."""
homepage = "https://www.cog-genomics.org/plink/1.9/"
version('1.9-beta5', '737545504ae19348a44a05fa69b75c28',
url='https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz')
version('1.07', 'fd0bafeda42151b20534e4f97b0d97df',
url='http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip',
preferred=True)
depends_on('atlas', when='@1.9-beta5')
depends_on('netlib-lapack', when='@1.9-beta5')
def install(self, spec, prefix):
mkdirp(prefix.bin)
if spec.version == Version('1.07'):
install('plink', prefix.bin)
install('gPLINK.jar', prefix.bin)
if spec.version == Version('1.9-beta5'):
with working_dir('1.9'):
first_compile = Executable('./plink_first_compile')
first_compile()
install('plink', prefix.bin)
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