From 1aed3f7c01bc6590618af5be79f0033a9cd44761 Mon Sep 17 00:00:00 2001 From: Douglas Duckworth Date: Thu, 14 Dec 2017 16:43:32 -0500 Subject: added breakdancer (#6319) --- .../repos/builtin/packages/breakdancer/package.py | 47 ++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/breakdancer/package.py diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py new file mode 100644 index 0000000000..4d8a2b80ca --- /dev/null +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -0,0 +1,47 @@ +############################################################################## +# 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 -- cgit v1.2.3-70-g09d2