kaks-calculator: new package (#5725)

* kaks-calculator: new package

* kaks-calculator: new package

* fixing homepage

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)