a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
45 lines
1.8 KiB
Python
45 lines
1.8 KiB
Python
# Copyright 2013-2021 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 Pagit(Package):
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"""PAGIT addresses the need for software to generate high quality draft
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genomes."""
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homepage = "http://www.sanger.ac.uk/science/tools/pagit"
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url = "ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V1.01.64bit.tgz"
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version('1.01', sha256='8069c1d236804cf4ea782495adcc50d18561ef466af06b21946b980b3c37ad55')
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depends_on('java', type=('build', 'run'))
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depends_on('perl', type=('build', 'run'))
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def install(self, spec, prefix):
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with working_dir('PAGIT'):
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install_tree('ABACAS', prefix.ABACAS)
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install_tree('bin', prefix.bin)
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install_tree('ICORN', prefix.ICORN)
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install_tree('IMAGE', prefix.IMAGE)
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install_tree('lib', prefix.lib)
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install_tree('RATT', prefix.RATT)
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def setup_run_environment(self, env):
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env.set('PAGIT_HOME', self.prefix)
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env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5'))
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env.set('ICORN_HOME', self.prefix.icorn)
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env.set('SNPOMATIC_HOME', self.prefix.bin)
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env.set('RATT_HOME', self.prefix.RATT)
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env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config'))
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env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5',
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'ssaha2'))
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env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5'))
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env.prepend_path('PATH', self.prefix.IMAGE)
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env.prepend_path('PATH', self.prefix.ABACAS)
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env.prepend_path('PATH', self.prefix.ICORN)
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env.prepend_path('PATH', self.prefix.RATT)
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env.prepend_path('PERL5LIB', self.prefix.lib)
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