breseq: Create new package (#6648)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 Breseq(AutotoolsPackage):
+    """breseq is a computational pipeline for finding mutations relative to a
+    reference sequence in short-read DNA re-sequencing data for haploid
+    microbial-sized genomes."""
+
+    homepage = "http://barricklab.org/breseq"
+    url      = "https://github.com/barricklab/breseq/archive/v0.31.1.tar.gz"
+
+    version('0.31.1', 'a4e602d5481f8692833ba3d5a3cd0394')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    depends_on('bedtools2', type='run')
+    depends_on('r', type='run')