80100ffc39
* treesub: new package starting at 0.2 * treesub: fix ant build, add exec script * treesub: use portable octal format * treesub: add license header not sure how it even went missing.
62 lines
2.4 KiB
Python
62 lines
2.4 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, 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 os
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class Treesub(Package):
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"""A small program (which glues together other programs) that
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allows a user to input a codon alignment in FASTA format and
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produce an annotated phylogenetic tree showing which substitutions
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occurred on a given branch. Originally written for colleagues at
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the MRC NIMR."""
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homepage = "https:/github.com/tamuri/treesub"
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url = "https://github.com/tamuri/treesub/archive/v0.2.tar.gz"
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version('0.2', sha256='58b0d2638cf9ae1ad8705df26a57c32b52a69f50e7954debbd678c82772fdc56')
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version('0.1', sha256='c083ecc5f7e9f11645a7e768f6a09fefcbb254b526212003527b4b8dd14723f1')
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depends_on('jdk', type='run')
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depends_on('ant', type='build')
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depends_on('paml', type='run')
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depends_on('raxml', type='run')
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depends_on('figtree', type='run')
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def install(self, spec, prefix):
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ant = self.spec['ant'].command
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ant('jar')
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mkdirp(prefix.bin)
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install_tree('dist', prefix.bin)
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mkdirp(prefix.lib)
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install_tree('lib', prefix.lib)
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execscript = join_path(self.package_dir, 'treesub')
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os.chmod(execscript, 0o775)
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install(execscript, prefix.bin)
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