added breakdancer (#6319)

1 files changed, 47 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py
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+++ b/var/spack/repos/builtin/packages/breakdancer/package.py
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+##############################################################################
+# 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 Breakdancer(CMakePackage):
+    """BreakDancer-1.3.6, released under GPLv3, is a Cpp package that provides
+    genome-wide detection of structural variants from next generation
+    paired-end sequencing reads. It includes two complementary programs.
+    BreakDancerMax predicts five types of structural variants: insertions,
+    deletions, inversions, inter- and intra-chromosomal translocations from
+    next-generation short paired-end sequencing reads using read pairs that are
+    mapped with unexpected separation distances or orientation.
+    BreakDancerMini focuses on detecting small indels (usually between 10bp and
+    100bp) using normally mapped read pairs.."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/breakdancer"
+    url      = "https://github.com/genome/breakdancer.git"
+
+    version('master', git='https://github.com/genome/breakdancer.git',
+            submodules='true')
+
+    depends_on('zlib')
+
+    parallel = False