79 lines
2.9 KiB
Python
79 lines
2.9 KiB
Python
# Copyright 2013-2021 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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import os
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from spack import *
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class Blasr(Package):
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"""The PacBio long read aligner."""
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homepage = "https://github.com/PacificBiosciences/blasr/wiki"
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url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
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version('5.3.1', sha256='ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049')
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depends_on('ncurses')
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depends_on('hdf5+cxx@1.8.12:1.8')
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depends_on('htslib')
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depends_on('zlib')
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depends_on('boost')
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depends_on('pbbam')
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depends_on('blasr-libcpp')
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depends_on('python', type='build')
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phases = ['configure', 'build', 'install']
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def setup_build_environment(self, env):
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env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
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env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.pbdata)
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env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.alignment)
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env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf)
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# hdf has +mpi by default, so handle that possibility
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if ('+mpi' in self.spec['hdf5']):
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env.set('CC', self.spec['mpi'].mpicc)
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env.set('CXX', self.spec['mpi'].mpicxx)
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def setup_run_environment(self, env):
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env.prepend_path('PATH', self.spec.prefix.utils)
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def configure(self, spec, prefix):
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configure_args = [
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'LIBPBDATA_INC={0}'.format(
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self.spec['blasr-libcpp'].prefix),
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'LIBPBDATA_LIB={0}'.format(
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self.spec['blasr-libcpp'].prefix.pbdata),
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'LIBBLASR_LIB={0}'.format(
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self.spec['blasr-libcpp'].prefix.alignment),
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'LIBBLASR_INC={0}'.format(
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self.spec['blasr-libcpp'].prefix),
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'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix),
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'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf),
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'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
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'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib),
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'--shared'
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]
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python('configure.py', *configure_args)
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def build(self, spec, prefix):
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os.environ['CPLUS_INCLUDE_PATH'] = join_path(
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self.stage.source_path, 'include')
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make()
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def install(self, spec, prefix):
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mkdir(prefix.utils)
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mkdir(prefix.bin)
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install('blasr', prefix.bin.blasr)
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install('utils/loadPulses', prefix.utils)
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install('utils/pls2fasta', prefix.utils)
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install('utils/samFilter', prefix.utils)
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install('utils/samtoh5', prefix.utils)
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install('utils/samtom4', prefix.utils)
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install('utils/sawriter', prefix.utils)
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install('utils/sdpMatcher', prefix.utils)
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install('utils/toAfg', prefix.utils)
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