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authorbecker33 <becker33@llnl.gov>2016-08-05 10:21:10 -0700
committerGitHub <noreply@github.com>2016-08-05 10:21:10 -0700
commitf403f256ca693350e6cda44b823a030f8970b28b (patch)
treebc7a253e4853ab7b1488407fc331da3d26c131e1 /var
parent594a6710ed798a473004a3d61c1d56cddfc3c22c (diff)
parentd4274b32f283a056bec7048f1ab8b78bf1518bb6 (diff)
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Merge pull request #1450 from hartzell/feature/add-package-for-bwa
Add package for bwa
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/bwa/package.py52
1 files changed, 52 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py
new file mode 100644
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+++ b/var/spack/repos/builtin/packages/bwa/package.py
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+##############################################################################
+# 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)