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# Copyright 2013-2019 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 GmapGsnap(AutotoolsPackage):
"""GMAP: A Genomic Mapping and Alignment Program for
mRNA and EST Sequences, and GSNAP: Genomic Short-read
Nucleotide Alignment Program"""
homepage = "http://research-pub.gene.com/gmap/"
url = "http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-16.tar.gz"
version('2019-05-12', sha256='3dc1b6ee4f6c049c07bcf4a5aba30eb2d732997241cdcad818dab571719f8008')
version('2019-02-15', sha256='7e82b9867a1e561b4816fb2f2fb916294077c384c6a88bb94cce39bfe71ab3ac')
version('2018-07-04', sha256='a9f8c1f0810df65b2a089dc10be79611026f4c95e4681dba98fea3d55d598d24')
version('2018-03-25', 'f08e65c1e4d9574a3eb7f15f8ca6af16')
version('2018-02-12', '13152aedeef9ac66be915fc6bf6464f2')
version('2017-06-16', 'fcc91b8bdd4bf12ae3124de0c00db0c0')
version('2014-12-28', '1ab07819c9e5b5b8970716165ccaa7da')
depends_on('zlib')
depends_on('bzip2')
variant(
'simd',
description='CPU support.',
values=('avx2', 'sse42', 'avx512', 'sse2'),
multi=True,
default='sse2'
)
def configure(self, spec, prefix):
configure = Executable('../configure')
for simd in spec.variants['simd'].value:
with working_dir(simd, create=True):
configure('--with-simd-level={0}'.format(simd),
'--prefix={0}'.format(prefix))
def build(self, spec, prefix):
for simd in spec.variants['simd'].value:
with working_dir(simd):
make()
def check(self):
for simd in self.spec.variants['simd'].value:
with working_dir(simd):
make('check')
def install(self, spec, prefix):
for simd in spec.variants['simd'].value:
with working_dir(simd):
make('install')
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