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# Copyright 2013-2021 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 *
import os
class BlasrLibcpp(Package):
"""Blasr_libcpp is a library used by blasr
and other executables such as samtoh5,
loadPulses for analyzing PacBio sequences."""
homepage = "https://github.com/PacificBiosciences/blasr_libcpp"
url = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz"
maintainers = ['robqiao']
version('5.3.1', sha256='45a673255bfe7e29ed1f5bdb6410aa45cb6b907400d038c3da9daf1058b09156')
depends_on('pbbam')
depends_on('hdf5+cxx@1.8.12:1.8.99')
# maximum version is 1.8.20 currently. There doesn't appear to be a
# major version 1.9 and the 1.10.1 version doesn't build correctly.
# https://github.com/PacificBiosciences/blasr/issues/355
depends_on('python@2.7:2.8', type='build')
phases = ['configure', 'build', 'install']
def configure(self, spec, prefix):
configure_args = [
'PBBAM_INC={0}'.format(self.spec['pbbam'].prefix.include),
'PBBAM_LIB={0}'.format(self.spec['pbbam'].prefix.lib),
'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib)
]
python('configure.py', *configure_args)
def build(self, spec, prefix):
os.environ['CPLUS_INCLUDE_PATH'] = self.stage.source_path
make()
def install(self, spec, prefix):
install_tree('alignment', prefix.alignment)
install_tree('hdf', prefix.hdf)
install_tree('pbdata', prefix.pbdata)
def setup_dependent_build_environment(self, env, dependent_spec):
env.prepend_path('LD_LIBRARY_PATH', self.spec.prefix.hdf)
env.prepend_path('LD_LIBRARY_PATH', self.spec.prefix.alignment)
env.prepend_path('LD_LIBRARY_PATH', self.spec.prefix.pbdata)
def setup_run_environment(self, env):
env.prepend_path('LD_LIBRARY_PATH',
self.spec['blasr-libcpp'].prefix.pbdata)
env.prepend_path('LD_LIBRARY_PATH',
self.spec['blasr-libcpp'].prefix.alignment)
env.prepend_path('LD_LIBRARY_PATH',
self.spec['blasr-libcpp'].prefix.hdf)
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