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-rw-r--r--var/spack/repos/builtin/packages/blasr-libcpp/package.py73
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diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
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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 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)