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
42 lines
1.4 KiB
Python
42 lines
1.4 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 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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