61 lines
2.6 KiB
Python
61 lines
2.6 KiB
Python
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##############################################################################
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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 distutils.dir_util import copy_tree, mkpath
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from distutils.file_util import copy_file
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class Fastqc(Package):
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"""A quality control tool for high throughput sequence data."""
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homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
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url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
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version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
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depends_on('jdk', type='run')
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depends_on('perl') # for fastqc "script", any perl will do
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patch('fastqc.patch', level=0)
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def install(self, spec, prefix):
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mkpath(self.prefix.bin)
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mkpath(self.prefix.lib)
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copy_file('fastqc', self.prefix.bin)
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for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
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copy_file(j, self.prefix.lib)
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for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
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copy_tree(d, join_path(self.prefix.lib, d))
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chmod = which('chmod')
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chmod('+x', join_path(self.prefix.bin, 'fastqc'))
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# In theory the 'run' dependency on 'jdk' above should take
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# care of this for me. In practice, it does not.
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def setup_environment(self, spack_env, env):
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"""Add <prefix> to the path; the package has a script at the
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top level.
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"""
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env.prepend_path('PATH', join_path(self.spec['jdk'].prefix, 'bin'))
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