eea786f4e8
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
62 lines
2.1 KiB
Python
62 lines
2.1 KiB
Python
# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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import inspect
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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('perl-text-soundex', 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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install_tree('.', prefix.bin)
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