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| -rw-r--r-- | var/spack/repos/builtin/packages/blasr-libcpp/package.py | 73 |
1 files changed, 73 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py new file mode 100644 index 0000000000..c597fae507 --- /dev/null +++ b/var/spack/repos/builtin/packages/blasr-libcpp/package.py @@ -0,0 +1,73 @@ +############################################################################## +# 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 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" + + version('5.3.1', 'ca770042cbca508d5ff12dff0d645045') + + 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', 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_environment(self, spack_env, run_env, dependent_spec): + spack_env.prepend_path('LD_LIBRARY_PATH', + self.spec.prefix.hdf) + spack_env.prepend_path('LD_LIBRARY_PATH', + self.spec.prefix.alignment) + spack_env.prepend_path('LD_LIBRARY_PATH', + self.spec.prefix.pbdata) |