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
48 lines
1.7 KiB
Python
48 lines
1.7 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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class Redundans(Package):
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"""Redundans pipeline assists an assembly of heterozygous genomes."""
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homepage = "https://github.com/Gabaldonlab/redundans"
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url = "https://github.com/Gabaldonlab/redundans/archive/v0.13c.tar.gz"
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git = "https://github.com/Gabaldonlab/redundans.git"
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version('0.14a', commit='a20215a862aed161cbfc79df9133206156a1e9f0')
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version('0.13c', sha256='26d48f27a32678d94c1d00cb3b8991d74891d6cad64a94569901ff9607a7a736')
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depends_on('python', type=('build', 'run'))
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depends_on('py-pyscaf', type=('build', 'run'))
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depends_on('py-fastaindex', type=('build', 'run'))
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depends_on('py-numpy', type=('build', 'run'))
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depends_on('perl', type=('build', 'run'))
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depends_on('sspace-standard')
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depends_on('bwa')
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depends_on('last')
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depends_on('gapcloser')
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depends_on('parallel')
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depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))
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def install(self, spec, prefix):
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sspace_location = join_path(spec['sspace-standard'].prefix,
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'SSPACE_Standard_v3.0.pl')
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filter_file(r'sspacebin = os.path.join(.*)$',
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'sspacebin = \'' + sspace_location + '\'',
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'redundans.py')
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binfiles = ['redundans.py', 'bin/filterReads.py']
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# new internal dep with 0.14a
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if spec.satisfies('@0.14a:'):
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binfiles.append('bin/denovo.py')
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mkdirp(prefix.bin)
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for f in binfiles:
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install(f, prefix.bin)
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install('bin/fast?2*.py', prefix.bin)
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