paml: new package (#5142)

var/spack/repos/builtin/packages/paml/package.py

@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 Paml(MakefilePackage):
+    """PAML is a package of programs for phylogenetic analyses of DNA or
+       protein sewuences using maximum likelihood."""
+
+    homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html"
+    url      = "http://abacus.gene.ucl.ac.uk/software/paml4.9e.tgz"
+
+    version('4.9e', 'ac5a062bfea1f4eaac79008434030acf')
+
+    build_directory = 'src'
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir(self.build_directory):
+            install('baseml', prefix.bin)
+            install('basemlg', prefix.bin)
+            install('chi2', prefix.bin)
+            install('codeml', prefix.bin)
+            install('evolver', prefix.bin)
+            install('infinitesites', prefix.bin)
+            install('mcmctree', prefix.bin)
+            install('pamp', prefix.bin)
+            install('yn00', prefix.bin)
+        install_tree('dat', prefix.dat)
+        install_tree('Technical', prefix.Technical)