62 lines
2.3 KiB
Python
62 lines
2.3 KiB
Python
# Copyright 2013-2020 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)
|