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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class KaksCalculator(MakefilePackage, SourceforgePackage):
"""KaKs_Calculator adopts model selection and model averaging to calculate
nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to
include as many features as needed for accurately capturing evolutionary
information in protein-coding sequences."""
homepage = "https://sourceforge.net/projects/kakscalculator2"
sourceforge_mirror_path = "kakscalculator2/KaKs_Calculator2.0.tar.gz"
version("2.0", sha256="e2df719a2fecc549d8ddc4e6d8f5cfa4b248282dca319c1928eaf886d68ec3c5")
build_directory = "src"
def url_for_version(self, version):
url = "https://downloads.sourceforge.net/project/kakscalculator2/KaKs_Calculator{0}.tar.gz"
return url.format(version)
# include<string.h> needs added to header file for compilation to work
def patch(self):
with working_dir(self.build_directory):
header = FileFilter("base.h")
header.filter("#include<time.h>", "#include<time.h>\n#include<string.h>")
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir(self.build_directory):
install("KaKs_Calculator", prefix.bin)
install("ConPairs", prefix.bin)
install("AXTConvertor", prefix.bin)
install_tree("doc", prefix.doc)
install_tree("examples", prefix.examples)
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