shortstack: new package (#4905)

var/spack/repos/builtin/packages/shortstack/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 Shortstack(Package):
+    """ShortStack is a tool developed to process and analyze smallRNA-seq data
+       with respect to a reference genome, and output a comprehensive and
+       informative annotation of all discovered small RNA genes."""
+
+    homepage = "http://sites.psu.edu/axtell/software/shortstack/"
+    url      = "https://github.com/MikeAxtell/ShortStack/archive/v3.8.3.tar.gz"
+
+    version('3.8.3', '3f21f494f799039f3fa88ea343f2d20d')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('samtools')
+    depends_on('viennarna')
+    depends_on('bowtie')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('ShortStack', prefix.bin)