abbc47823d
* SourceForge: Mirror Mixin Add a mixing class for direct `CNAME`s to sourceforge mirrors. Since the main gateway servers are often down, this could reduce timeouts and fetch errors for sourceforge.net hosted software. * SourceForge: unspectacular mirror replacement add mirrors to all sourceforge packages with trivial download logic. tested fetch of latest version of each of these packages with various mirrors before committing. * SourceForge: xz the author homepage is chronocially overrun and this is the offical upload with many mirrors.
41 lines
1.6 KiB
Python
41 lines
1.6 KiB
Python
# Copyright 2013-2020 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 KaksCalculator(MakefilePackage, SourceforgePackage):
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"""KaKs_Calculator adopts model selection and model averaging to calculate
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nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to
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include as many features as needed for accurately capturing evolutionary
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information in protein-coding sequences."""
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homepage = "https://sourceforge.net/projects/kakscalculator2"
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sourceforge_mirror_path = "kakscalculator2/KaKs_Calculator2.0.tar.gz"
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version('2.0', sha256='e2df719a2fecc549d8ddc4e6d8f5cfa4b248282dca319c1928eaf886d68ec3c5')
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build_directory = 'src'
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def url_for_version(self, version):
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url = 'https://downloads.sourceforge.net/project/kakscalculator2/KaKs_Calculator{0}.tar.gz'
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return url.format(version)
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# include<string.h> needs added to header file for compilation to work
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def patch(self):
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with working_dir(self.build_directory):
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header = FileFilter('base.h')
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header.filter('#include<time.h>',
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'#include<time.h>\n#include<string.h>')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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with working_dir(self.build_directory):
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install('KaKs_Calculator', prefix.bin)
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install('ConPairs', prefix.bin)
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install('AXTConvertor', prefix.bin)
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install_tree('doc', prefix.doc)
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install_tree('examples', prefix.examples)
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