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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Portcullis(AutotoolsPackage):
"""PORTable CULLing of Invalid Splice junctions"""
homepage = "https://github.com/maplesond/portcullis"
url = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz"
version('1.1.2', '5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749')
depends_on('autoconf@2.53:', type='build')
depends_on('automake@1.11:', type='build')
depends_on('libtool@2.4.2:', type='build')
depends_on('m4', type='build')
depends_on('zlib', type='build')
depends_on('samtools', type='build')
depends_on('python@3.4:', type=('build', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-pandas', type=('build', 'run'))
# later versions of py-sphinx don't get detected by the configure script
depends_on('py-sphinx@1.3:1.4')
def patch(self):
# remove static linking to libstdc++
filter_file(
'AM_LDFLAGS="-static-libstdc++"',
'AM_LDFLAGS=""',
'configure.ac', string=True
)
# prevent install scripts from ruining our PYTHONPATH
filter_file(
'export PYTHONPATH=$(DESTDIR)$(pythondir)',
'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
'scripts/Makefile.am', string=True
)
# remove -m64 on aarch64
if self.spec.target.family == 'aarch64':
for f in ['lib/Makefile.am', 'src/Makefile.am']:
filter_file('-m64', '', f)
def build(self, spec, prefix):
# build manpages
make('man')
# run boost build script
sh = which('sh')
sh('build_boost.sh')
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