81 lines
3.1 KiB
Python
81 lines
3.1 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/spack/spack
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# Please also see the NOTICE and LICENSE files 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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import inspect
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import distutils.dir_util
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class Repeatmasker(Package):
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"""RepeatMasker is a program that screens DNA sequences for interspersed
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repeats and low complexity DNA sequences."""
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homepage = "http://www.repeatmasker.org"
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url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
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version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
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depends_on('perl', type=('build', 'run'))
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depends_on('hmmer')
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depends_on('ncbi-rmblastn')
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depends_on('trf')
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def url_for_version(self, version):
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url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
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return url.format(version.dashed)
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def install(self, spec, prefix):
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# Config questions consist of:
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#
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# <PRESS ENTER TO CONTINUE>
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# Enter perl path
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# Enter where repeatmasker is being configured from
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# Enter trf path
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# Add a Search Engine:
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# 1. CrossMatch
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# 2. RMBlast - NCBI Blast with RepeatMasker extensions
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# 3. WUBlast/ABBlast (required by DupMasker)
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# 4. HMMER3.1 & DFAM
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# 5. Done
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# Enter RMBlast path
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# Do you want RMBlast to be your default search engine for
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# Repeatmasker? (Y/N)
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# Add a Search Engine: Done
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config_answers = ['\n', '%s\n' % self.spec['perl'].command.path,
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'%s\n' % self.stage.source_path,
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'%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
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'%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
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'Y\n', '5\n']
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config_answers_filename = 'spack-config.in'
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with open(config_answers_filename, 'w') as f:
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f.writelines(config_answers)
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with open(config_answers_filename, 'r') as f:
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inspect.getmodule(self).perl('configure', input=f)
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distutils.dir_util.copy_tree(".", prefix)
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