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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
##
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
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', '53c93f499aa4bc10781c87bafc33df2a')
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_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', self.spec.prefix.utils)
spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
spack_env.prepend_path('CPATH', self.spec[
'blasr-libcpp'].prefix.pbdata)
spack_env.prepend_path('CPATH', self.spec[
'blasr-libcpp'].prefix.alignment)
spack_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']):
spack_env.set('CC', self.spec['mpi'].mpicc)
spack_env.set('CXX', self.spec['mpi'].mpicxx)
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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