stacks: new package (#4875)

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

@@ -0,0 +1,48 @@
+##############################################################################
+# 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 Stacks(AutotoolsPackage):
+    """Stacks is a software pipeline for building loci from short-read
+       sequences, such as those generated on the Illumina platform."""
+
+    homepage = "http://catchenlab.life.illinois.edu/stacks/"
+    url      = "http://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz"
+
+    version('1.46', '18b0568a4bba44fb4e5be0eb7ee2c08d')
+
+    variant('sparsehash', default=True, description='Improve Stacks memory usage with SparseHash')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('sparsehash', when='+sparsehash')
+
+    def configure_args(self):
+        args = []
+        if '+sparsehash' in self.spec:
+            args.append('--enable-sparsehash')
+        else:
+            args.append('--disable-sparsehash')
+        return args