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
38 lines
1.3 KiB
Python
38 lines
1.3 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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class Snphylo(Package):
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"""A pipeline to generate a phylogenetic tree from huge SNP data"""
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homepage = "http://chibba.pgml.uga.edu/snphylo/"
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url = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
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version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
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depends_on('python', type=('build', 'run'))
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depends_on('r', type=('build', 'run'))
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depends_on('r-phangorn', type=('build', 'run'))
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depends_on('r-gdsfmt', type=('build', 'run'))
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depends_on('r-snprelate', type=('build', 'run'))
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depends_on('r-getopt', type=('build', 'run'))
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depends_on('muscle')
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depends_on('phylip')
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def install(self, spec, prefix):
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install_answer = ['y', 'y', 'y', 'y']
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install_answer_input = 'spack-config.in'
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with open(install_answer_input, 'w') as f:
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f.writelines(install_answer)
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with open(install_answer_input, 'r') as f:
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bash = which('bash')
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bash('./setup.sh', input=f)
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install_tree('.', prefix)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PATH', self.spec.prefix)
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