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# Copyright 2013-2022 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.package import *
class Bowtie2(MakefilePackage):
"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences"""
homepage = "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
version('2.4.2', sha256='4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e')
version('2.4.1', sha256='566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22')
version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc')
version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443')
version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c')
version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0')
depends_on('tbb', when='@2.3.0:')
depends_on('readline', when='@2.3.1:')
depends_on('perl', type='run')
depends_on('python', type='run')
depends_on('zlib', when='@2.3.1:')
depends_on('simde', when='@2.4.0: target=aarch64:', type='link')
depends_on('simde', when='@2.4.0: target=ppc64le:', type='link')
patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
# seems to have trouble with 6's -std=gnu++14
conflicts('%gcc@6:', when='@:2.3.1')
conflicts('^intel-oneapi-tbb', when='@:2.3.5.1')
conflicts('@:2.3.5.0', when='target=aarch64:')
conflicts('@2.4.1', when='target=aarch64:')
def edit(self, spec, prefix):
kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
match = '^#!/usr/bin/env perl'
perl = spec['perl'].command
substitute = "#!{perl}".format(perl=perl)
files = ['bowtie2', ]
filter_file(match, substitute, *files, **kwargs)
match = '^#!/usr/bin/env python.*'
python = spec['python'].command
substitute = "#!{python}".format(python=python)
files = ['bowtie2-build', 'bowtie2-inspect']
filter_file(match, substitute, *files, **kwargs)
if (self.spec.satisfies('@2.4.0:2.4.2 target=aarch64:') or
self.spec.satisfies('@2.4.0:2.4.2 target=ppc64le:')):
match = '-Ithird_party/simde'
simdepath = spec['simde'].prefix.include
substitute = "-I{simdepath}".format(simdepath=simdepath)
files = ['Makefile']
filter_file(match, substitute, *files, **kwargs)
@property
def build_targets(self):
make_arg = ['PREFIX={0}'.format(self.prefix)]
if self.spec.satisfies('target=aarch64:'):
make_arg.append('POPCNT_CAPABILITY=0')
return make_arg
@property
def install_targets(self):
if self.spec.satisfies('@:2.3.9'):
return ['prefix={0}'.format(self.prefix), 'install']
else:
return ['PREFIX={0}'.format(self.prefix), 'install']
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