9385659aa1
* Add support for 2.3.1 Updated digest and added a dependency on tbb. * Cleanup patch name and add description
59 lines
2.4 KiB
Python
59 lines
2.4 KiB
Python
##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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from glob import glob
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class Bowtie2(Package):
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"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
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sequencing reads to long reference sequences"""
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homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
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version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
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version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
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depends_on('tbb', when='@2.3.1')
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patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
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patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
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def url_for_version(self, version):
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url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{0}/bowtie2-{0}-source.zip"
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return url.format(version)
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def install(self, spec, prefix):
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make()
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mkdirp(prefix.bin)
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for bow in glob("bowtie2*"):
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install(bow, prefix.bin)
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# install('bowtie2',prefix.bin)
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# install('bowtie2-align-l',prefix.bin)
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# install('bowtie2-align-s',prefix.bin)
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# install('bowtie2-build',prefix.bin)
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# install('bowtie2-build-l',prefix.bin)
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# install('bowtie2-build-s',prefix.bin)
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# install('bowtie2-inspect',prefix.bin)
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# install('bowtie2-inspect-l',prefix.bin)
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# install('bowtie2-inspect-s',prefix.bin)
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