microbiomeutil: new package (#5134)

* microbiomeutil: new package

* got rid of unnecessary self

* oops

1 files changed, 53 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/microbiomeutil/package.py b/var/spack/repos/builtin/packages/microbiomeutil/package.py
new file mode 100644
index 0000000000..7be7a4ac0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/microbiomeutil/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# 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 Microbiomeutil(MakefilePackage):
+    """Microbiome analysis utilities"""
+
+    homepage = "http://microbiomeutil.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/microbiomeutil/microbiomeutil-r20110519.tgz"
+
+    version('20110519', '11eaac4b0468c05297ba88ec27bd4b56')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('blast-plus')
+    depends_on('cdbfasta')
+
+    def install(self, spec, prefix):
+        install_tree('ChimeraSlayer', prefix.ChimeraSlayer)
+        install_tree('NAST-iEr', join_path(prefix, 'NAST-iEr'))
+        install_tree('TreeChopper', prefix.TreeChopper)
+        install_tree('WigeoN', prefix.WigeoN)
+        install_tree('docs', prefix.docs)
+        install_tree('RESOURCES', prefix.resources)
+        install_tree('AmosCmp16Spipeline', prefix.AmosCmp16Spipeline)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.ChimeraSlayer)
+        run_env.prepend_path('PATH', join_path(self.prefix, 'NAST-iEr'))
+        run_env.prepend_path('PATH', self.prefix.TreeChopper)
+        run_env.prepend_path('PATH', self.prefix.WigeoN)