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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/blasr/package.py | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py new file mode 100644 index 0000000000..b7f100b642 --- /dev/null +++ b/var/spack/repos/builtin/packages/blasr/package.py @@ -0,0 +1,96 @@ +############################################################################## +# 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) |