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# Copyright 2013-2021 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 Soapdenovo2(MakefilePackage):
"""SOAPdenovo is a novel short-read assembly method that can build a de
novo draft assembly for the human-sized genomes. The program is
specially designed to assemble Illumina GA short reads. It creates
new opportunities for building reference sequences and carrying out
accurate analyses of unexplored genomes in a cost effective way."""
homepage = "https://github.com/aquaskyline/SOAPdenovo2"
url = "https://github.com/aquaskyline/SOAPdenovo2/archive/r240.tar.gz"
version('242', sha256='a0043ceb41bc17a1c3fd2b8abe4f9029a60ad3edceb2b15af3c2cfabd36aa11b')
version('240', sha256='cc9e9f216072c0bbcace5efdead947e1c3f41f09baec5508c7b90f933a090909')
def flag_handler(self, name, flags):
if self.spec.satisfies('%gcc@10:'):
if name == 'cflags' or name == 'CFLAGS':
flags.append('-fcommon')
if name == 'cxxflags' or name == 'CXXFLAGS':
flags.append('-fcommon')
return (flags, None, None)
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('SOAPdenovo-63mer', prefix.bin)
install('SOAPdenovo-127mer', prefix.bin)
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