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authorAudrey Thoma <las_thoma15@iastate.edu>2017-07-24 19:50:40 -0500
committerAdam J. Stewart <ajstewart426@gmail.com>2017-07-24 19:50:40 -0500
commit4237e5fffd71841b973f3a6b76604cc13fccc4cd (patch)
treec5c7d599b52b2d9eed9347957e9e3d87ce94ea63 /var
parent07e60bc26bd9f12cff2fde93c31f4b6560614f96 (diff)
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stacks: new package (#4875)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/stacks/package.py48
1 files changed, 48 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/stacks/package.py b/var/spack/repos/builtin/packages/stacks/package.py
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+++ b/var/spack/repos/builtin/packages/stacks/package.py
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+##############################################################################
+# 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