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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 *
from glob import glob
class Bowtie2(Package):
"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
sequencing reads to long reference sequences"""
homepage = "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('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9')
version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
version('2.3.0', '3ab33f30f00f3c30fec1355b4e569ea2')
version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
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:')
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')
@run_before('install')
def filter_sbang(self):
"""Run before install so that the standard Spack sbang install hook
can fix up the path to the perl|python binary.
"""
with working_dir(self.stage.source_path):
kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
match = '^#!/usr/bin/env perl'
perl = self.spec['perl'].command
substitute = "#!{perl}".format(perl=perl)
files = ['bowtie2', ]
filter_file(match, substitute, *files, **kwargs)
match = '^#!/usr/bin/env python'
python = self.spec['python'].command
substitute = "#!{python}".format(python=python)
files = ['bowtie2-build', 'bowtie2-inspect']
filter_file(match, substitute, *files, **kwargs)
def install(self, spec, prefix):
make()
mkdirp(prefix.bin)
for bow in glob("bowtie2*"):
install(bow, prefix.bin)
# install('bowtie2',prefix.bin)
# install('bowtie2-align-l',prefix.bin)
# install('bowtie2-align-s',prefix.bin)
# install('bowtie2-build',prefix.bin)
# install('bowtie2-build-l',prefix.bin)
# install('bowtie2-build-s',prefix.bin)
# install('bowtie2-inspect',prefix.bin)
# install('bowtie2-inspect-l',prefix.bin)
# install('bowtie2-inspect-s',prefix.bin)
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