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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)
import os
from spack import *
class Blasr(Package):
"""The PacBio long read aligner."""
homepage = "https://github.com/PacificBiosciences/blasr/wiki"
url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
version('5.3.1', sha256='ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049')
depends_on('ncurses')
depends_on('hdf5+cxx@1.8.12:1.8.99')
depends_on('htslib')
depends_on('zlib')
depends_on('boost')
depends_on('pbbam')
depends_on('blasr-libcpp')
depends_on('python', type='build')
phases = ['configure', 'build', 'install']
def setup_build_environment(self, env):
env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.pbdata)
env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.alignment)
env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf)
# hdf has +mpi by default, so handle that possibility
if ('+mpi' in self.spec['hdf5']):
env.set('CC', self.spec['mpi'].mpicc)
env.set('CXX', self.spec['mpi'].mpicxx)
def setup_run_environment(self, env):
env.prepend_path('PATH', self.spec.prefix.utils)
def configure(self, spec, prefix):
configure_args = [
'LIBPBDATA_INC={0}'.format(
self.spec['blasr-libcpp'].prefix),
'LIBPBDATA_LIB={0}'.format(
self.spec['blasr-libcpp'].prefix.pbdata),
'LIBBLASR_LIB={0}'.format(
self.spec['blasr-libcpp'].prefix.alignment),
'LIBBLASR_INC={0}'.format(
self.spec['blasr-libcpp'].prefix),
'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix),
'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf),
'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib),
'--shared'
]
python('configure.py', *configure_args)
def build(self, spec, prefix):
os.environ['CPLUS_INCLUDE_PATH'] = join_path(
self.stage.source_path, 'include')
make()
def install(self, spec, prefix):
mkdir(prefix.utils)
mkdir(prefix.bin)
install('blasr', prefix.bin.blasr)
install('utils/loadPulses', prefix.utils)
install('utils/pls2fasta', prefix.utils)
install('utils/samFilter', prefix.utils)
install('utils/samtoh5', prefix.utils)
install('utils/samtom4', prefix.utils)
install('utils/sawriter', prefix.utils)
install('utils/sdpMatcher', prefix.utils)
install('utils/toAfg', prefix.utils)
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