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| -rw-r--r-- | var/spack/repos/builtin/packages/kaks-calculator/package.py | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/kaks-calculator/package.py b/var/spack/repos/builtin/packages/kaks-calculator/package.py new file mode 100644 index 0000000000..e57b41fbac --- /dev/null +++ b/var/spack/repos/builtin/packages/kaks-calculator/package.py @@ -0,0 +1,59 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class KaksCalculator(MakefilePackage): + """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" + url = "https://downloads.sourceforge.net/project/kakscalculator2/KaKs_Calculator2.0.tar.gz" + + version('2.0', '956ec7bdb30fac7da3b5b2563151a85e') + + 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) |