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/itsx/package.py

@@ -0,0 +1,44 @@
+##############################################################################
+# 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 Itsx(Package):
+    """Improved software detection and extraction of ITS1 and ITS2 from
+       ribosomal ITS sequences of fungi and other eukaryotes for use in
+       environmental sequencing"""
+
+    homepage = "http://microbiology.se/software/itsx/"
+    url      = "http://microbiology.se/sw/ITSx_1.0.11.tar.gz"
+
+    version('1.0.11', '1bff12f1d5742f19be6ca585e9bf81fa')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('hmmer')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('ITSx', prefix.bin)
+        install_tree('ITSx_db', prefix.bin.ITSx_db)