Add package sga. (#3330)

1 files changed, 61 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/sga/package.py b/var/spack/repos/builtin/packages/sga/package.py
new file mode 100644
index 0000000000..41e1830de1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sga/package.py
@@ -0,0 +1,61 @@
+##############################################################################
+# 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 LICENSE file 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 Sga(AutotoolsPackage):
+    """SGA is a de novo genome assembler based on the concept of string graphs.
+       The major goal of SGA is to be very memory efficient, which is achieved 
+       by using a compressed representation of DNA sequence reads."""
+
+    homepage = "https://www.msi.umn.edu/sw/sga"
+    url      = "https://github.com/jts/sga/archive/v0.10.15.tar.gz"
+
+    version('0.10.15', '990aed1593f8072650c6366e5cf32519')
+    version('0.10.14', '211edb372898d6515dcde98d17078b7b')
+    version('0.10.13', 'd4f6aefc48c940dba96cc6513649ecdd')
+    version('0.10.12', '993bc165b4c77b75a5a2fe01c200c0da')
+    version('0.10.11', 'b649da5471209f50df2d53f0f2bfa0ed')
+    version('0.10.10', '494ff18d82b34cdaf8432b48b0356aae')
+    version('0.10.9',  'c2111bfd278d8faaab19732aec79fa78')
+    version('0.10.8',  '4d75f836eaae6018d993a0b75326014a')
+    version('0.10.3',  'b12d35b24ca8a63c4dcc9f5d7e7c4133')
+
+    depends_on('zlib')
+    depends_on('sparsehash')
+    depends_on('jemalloc')
+    depends_on('bamtools')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+
+    configure_directory = 'src'
+
+    def configure_args(self):
+        return [
+            '--with-sparsehash={0}'.format(self.spec['sparsehash'].prefix),
+            '--with-bamtools={0}'.format(self.spec['bamtools'].prefix),
+            '--with-jemalloc={0}'.format(self.spec['jemalloc'].prefix)
+        ]