6b9d485e06
I've had non-repeatable failures in my CI runs on all three clusters at the bamutil's step. In each case there are .o or .so files that are corrupt or truncated. I suspect that the homebrewed bamutil Makefile scheme doesn't actually support parallel builds.
48 lines
1.9 KiB
Python
48 lines
1.9 KiB
Python
##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Bamutil(MakefilePackage):
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"""bamUtil is a repository that contains several programs
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that perform operations on SAM/BAM files. All of these programs
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are built into a single executable, bam.
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"""
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homepage = "http://genome.sph.umich.edu/wiki/BamUtil"
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url = "http://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
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version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79')
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# Looks like this will be fixed in 1.0.14.
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# https://github.com/statgen/libStatGen/issues/9
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patch('libstatgen-issue-9.patch', when='@1.0.13:')
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parallel = False
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@property
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def install_targets(self):
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return ['install', 'INSTALLDIR={0}'.format(self.prefix.bin)]
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