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
49 lines
1.7 KiB
Python
49 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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from spack import *
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class Kallisto(CMakePackage):
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"""kallisto is a program for quantifying abundances of transcripts from
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RNA-Seq data."""
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homepage = "http://pachterlab.github.io/kallisto"
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url = "https://github.com/pachterlab/kallisto/archive/v0.43.1.tar.gz"
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version('0.46.2', sha256='c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
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version('0.43.1', sha256='7baef1b3b67bcf81dc7c604db2ef30f5520b48d532bf28ec26331cb60ce69400')
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depends_on('zlib')
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depends_on('hdf5')
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# htslib isn't built in time to be used....
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parallel = False
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# v0.44.0 vendored a copy of htslib and uses auto* to build
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# its configure script.
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depends_on('autoconf', type='build', when='@0.44.0:')
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depends_on('automake', type='build', when='@0.44.0:')
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depends_on('libtool', type='build', when='@0.44.0:')
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depends_on('m4', type='build', when='@0.44.0:')
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# Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args
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# causes bits of cmake's output to end up in the autoconf-generated
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# configure script.
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# See https://github.com/spack/spack/issues/15274 and
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# https://github.com/pachterlab/kallisto/issues/253
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@property
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def std_cmake_args(self):
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"""Call the original std_cmake_args and then filter the verbose
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setting.
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"""
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a = super(Kallisto, self).std_cmake_args
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if (self.spec.version >= Version('0.44.0')):
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args = [i for i in a if i != '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']
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else:
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args = a
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return args
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