pipits: new package (#5041)

* pipits: new package and dependencies

* fixing rdp-classifier java dep

* adding resources to pipits and fixing deps for py-biom-format

var/spack/repos/builtin/packages/rdp-classifier/package.py

@@ -0,0 +1,45 @@
+##############################################################################
+# 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 RdpClassifier(Package):
+    """The RDP Classifier is a naive Bayesian classifier that can rapidly and
+       accurately provides taxonomic assignments from domain to genus, with
+       confidence estimates for each assignment. """
+
+    homepage = "http://rdp.cme.msu.edu/"
+    url      = "https://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.12.zip"
+
+    version('2.12', '7fdfa33512629810f0ff06b905642ddd')
+
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install(join_path('dist', 'classifier.jar'), prefix.bin)
+        install_tree(join_path('dist', 'lib'), prefix.bin.lib)
+        install(join_path('lib', 'junit-4.8.2.jar'), prefix.bin.lib)
+        install_tree('src', prefix.src)