60 lines
1.9 KiB
Python
60 lines
1.9 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Portcullis(AutotoolsPackage):
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"""PORTable CULLing of Invalid Splice junctions"""
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homepage = "https://github.com/maplesond/portcullis"
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url = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz"
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version('1.1.2', sha256='5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749')
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depends_on('autoconf@2.53:', type='build')
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depends_on('automake@1.11:', type='build')
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depends_on('libtool@2.4.2:', type='build')
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depends_on('m4', type='build')
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depends_on('zlib', type='build')
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depends_on('samtools', type='build')
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depends_on('python@3.4:', type=('build', 'run'))
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depends_on('py-setuptools', type=('build', 'run'))
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depends_on('py-pandas', type=('build', 'run'))
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# later versions of py-sphinx don't get detected by the configure script
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depends_on('py-sphinx@1.3:1.4')
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def patch(self):
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# remove static linking to libstdc++
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filter_file(
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'AM_LDFLAGS="-static-libstdc++"',
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'AM_LDFLAGS=""',
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'configure.ac', string=True
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)
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# prevent install scripts from ruining our PYTHONPATH
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filter_file(
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'export PYTHONPATH=$(DESTDIR)$(pythondir)',
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'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
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'scripts/Makefile.am', string=True
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)
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# remove -m64 on aarch64
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if self.spec.target.family == 'aarch64':
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for f in ['lib/Makefile.am', 'src/Makefile.am']:
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filter_file('-m64', '', f)
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def build(self, spec, prefix):
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# build manpages
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make('man')
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# run boost build script
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sh = which('sh')
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sh('build_boost.sh')
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