mothur: new package (#5055)

* mothur: new package

* fixing mpi things

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

@@ -0,0 +1,59 @@
+##############################################################################
+# 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 Mothur(MakefilePackage):
+    """This project seeks to develop a single piece of open-source, expandable
+       software to fill the bioinformatics needs of the microbial ecology
+       community."""
+
+    homepage = "https://github.com/mothur/mothur"
+    url      = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz"
+
+    version('1.39.5', '1f826ea4420e6822fc0db002c5940b92')
+
+    variant('mpi', default=True, description='Enable MPI parallel support')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('boost')
+    depends_on('readline')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('BOOST_LIBRARY_DIR=\"\\\"Enter_your_boost_library_path'
+                        '_here\\\"\"', 'BOOST_LIBRARY_DIR=%s' %
+                        self.spec['boost'].prefix.lib)
+        makefile.filter('BOOST_INCLUDE_DIR=\"\\\"Enter_your_boost_include_path'
+                        '_here\\\"\"', 'BOOST_INCLUDE_DIR=%s' %
+                        self.spec['boost'].prefix.include)
+        makefile.filter('MOTHUR_FILES=\"\\\"Enter_your_default_path_'
+                        'here\\\"\"', 'MOTHUR_FILES=%s' % prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('mothur', prefix.bin)
+        install('uchime', prefix.bin)
+        install_tree('source', prefix.include)