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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 Bowtie(MakefilePackage):
"""Bowtie is an ultrafast, memory-efficient short read aligner
for short DNA sequences (reads) from next-gen sequencers."""
homepage = "https://sourceforge.net/projects/bowtie-bio/"
url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823')
# The bowtie project git tagged and GitHub released a v1.2.2,
# discovered/fixed a bug, git tagged a v1.2.2_p1 and moved the
# 1.2.2 release to use it rather than making a new `1.2.2_p1`
# release.
#
# We point both of the Spack versions at the same tarball so they
# build the binaries that are on the release page as v1.2.2
version('1.2.2_p1', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1')
version('1.2.2', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1', url="https://github.com/BenLangmead/bowtie/archive/v1.2.2_p1.tar.gz")
version('1.2.1.1', sha256='1b38408b88f61d18d7ff28b2470a8cfeefccb3fc59fd46e4cc62e23874e52c20')
version('1.2.1', sha256='b2a7c8c879cb08f00a82665bee43e1d4861de44a87912c54d168e44c90869728')
version('1.2.0', sha256='dc4e7951b8eca56ce7714c47fd4e84f72badd5312ee9546c912af1963570f894')
# Keeping the old 1.2 version around for reproducibility, it's not
# clearly identical to 1.2.0.
version('1.2', md5='6d97f0ea1a65af11d17cc270cfac4af9', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')
# 1.2.2 and 1.2.2_p1 fail to build with %gcc@8.3.0
# with and without issue-87 patch
conflicts('%gcc@8:', when='@1.2.2')
conflicts('%gcc@8:', when='@1.2.2_p1')
variant('tbb', default=False, description='Use Intel thread building block')
depends_on('tbb', when='+tbb')
depends_on('zlib')
# See: https://github.com/BenLangmead/bowtie/issues/87, a
# different fix is in the FreeBSD ports/package tree
# https://svnweb.freebsd.org/ports?view=revision&revision=483954
patch('issue-87.patch', when='@:1.2.2 %gcc@8.0.0:')
# correspond to 'aarch64' architecture
# reference: https://github.com/BenLangmead/bowtie/pull/13
patch('for_aarch64.patch', when='target=aarch64:')
# measures for narrowing error
patch('fix_narrowing_err.patch')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
makefile.filter('CC = .*', 'CC = ' + env['CC'])
makefile.filter('CXX = .*', 'CPP = ' + env['CXX'])
def build(self, spec, prefix):
if '+tbb' in spec:
make()
else:
make('NO_TBB=1')
def install(self, spec, prefix):
make('prefix={0}'.format(self.prefix), 'install')
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