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
71 lines
2.7 KiB
Python
71 lines
2.7 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 Biopieces(Package):
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"""The Biopieces are a collection of bioinformatics tools that can be
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pieced together in a very easy and flexible manner to perform both
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simple and complex tasks."""
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homepage = "http://maasha.github.io/biopieces/"
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git = "https://github.com/maasha/biopieces.git"
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version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856',
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submodules=True)
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-module-build', type=('build', 'run'))
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depends_on('perl-bit-vector', type=('build', 'run'))
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depends_on('perl-svg', type=('build', 'run'))
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depends_on('perl-term-readkey', type=('build', 'run'))
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depends_on('perl-time-hires', type=('build', 'run'))
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depends_on('perl-dbi', type=('build', 'run'))
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depends_on('perl-xml-parser', type=('build', 'run'))
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depends_on('perl-carp-clan', type=('build', 'run'))
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depends_on('perl-class-inspector', type=('build', 'run'))
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depends_on('perl-html-parser', type=('build', 'run'))
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depends_on('perl-lwp', type=('build', 'run'))
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depends_on('perl-soap-lite', type=('build', 'run'))
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depends_on('perl-uri', type=('build', 'run'))
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depends_on('perl-inline', type=('build', 'run'))
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depends_on('perl-inline-c', type=('build', 'run'))
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depends_on('perl-parse-recdescent', type=('build', 'run'))
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depends_on('perl-version', type=('build', 'run'))
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depends_on('perl-dbfile', type=('build', 'run'))
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depends_on('perl-dbd-mysql', type=('build', 'run'))
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depends_on('ruby@1.9:')
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depends_on('ruby-gnuplot')
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depends_on('ruby-narray')
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depends_on('ruby-rubyinline')
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depends_on('ruby-terminal-table')
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depends_on('python@2.6:', type=('build', 'run'))
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depends_on('blast-plus')
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depends_on('muscle')
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depends_on('mummer')
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depends_on('blat')
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depends_on('vmatch')
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depends_on('bowtie')
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depends_on('bwa')
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depends_on('usearch')
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depends_on('velvet')
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depends_on('idba')
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depends_on('ray')
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depends_on('scan-for-matches')
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def install(self, spec, prefix):
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install_tree('.', prefix)
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def setup_environment(self, spack_env, run_env):
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# Note: user will need to set environment variables on their own,
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# dependent on where they will want data to be located:
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# BP_DATA - Contains genomic data etc.
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# BP_TMP - Required temporary directory
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# BP_LOG - Required log directory
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run_env.prepend_path('BP_DIR', prefix)
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