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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Glfmultiples(MakefilePackage):
"""glfMultiples is a GLF-based variant caller for next-generation
sequencing data. It takes a set of GLF format genotype likelihood
files as input and generates a VCF-format set of variant calls
as output. """
homepage = "https://genome.sph.umich.edu/wiki/GlfMultiples"
url = "http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz"
version('2010-06-16', '64bf6bb7c76543f4c8fabce015a3cb11')
depends_on('zlib')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
makefile.filter('CXX=.*', 'CXX = ' + env['CXX'])
makefile.filter('CFLAGS=.*',
'CFLAGS=-O2 -I./libsrc -I./pdf ' +
'-D_FILE_OFFSET_BITS=64 -D__USE_LONG_INT')
def install(self, spec, prefix):
make('INSTALLDIR=%s' % prefix, 'install')
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