From d4274b32f283a056bec7048f1ab8b78bf1518bb6 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 26 Jul 2016 17:16:12 -0400 Subject: Make flake8 happy (long lines) --- var/spack/repos/builtin/packages/bwa/package.py | 52 +++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bwa/package.py diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py new file mode 100644 index 0000000000..bb6763629b --- /dev/null +++ b/var/spack/repos/builtin/packages/bwa/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 Bwa(Package): + """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.""" + + homepage = "http://github.com/lh3/bwa" + url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2" + + version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554') + + depends_on('zlib') + + def install(self, spec, prefix): + filter_file(r'^INCLUDES=', + "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile') + filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib, + 'Makefile') + make() + + mkdirp(prefix.bin) + install('bwa', join_path(prefix.bin, 'bwa')) + set_executable(join_path(prefix.bin, 'bwa')) + mkdirp(prefix.doc) + install('README.md', prefix.doc) + install('NEWS.md', prefix.doc) + mkdirp(prefix.man1) + install('bwa.1', prefix.man1) -- cgit v1.2.3-60-g2f50