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pbbam: new package (#8365)

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* pbbam: new package

* pbbam: updated version

* pbbam: added option tests handling

* pbbam: flake8 edits
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Miles Perry 2018-06-07 22:44:30 -05:00 committed by Adam J. Stewart
parent c8a3a650fa
commit 21ff3c9ac1
1 changed files with 62 additions and 0 deletions
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var/spack/repos/builtin/packages/pbbam/package.py Normal file
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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 *
class Pbbam(CMakePackage):
"""The pbbam software package provides components to create, query,
& edit PacBio BAM files and associated indices.
These components include a core C++ library,
bindings for additional languages, and command-line utilities."""
homepage = "https://github.com/PacificBiosciences/pbbam"
url = "https://github.com/PacificBiosciences/pbbam/archive/0.18.0.tar.gz"
version('0.18.0', 'abbb687b1e7ea08916c26da828e11384')
depends_on('zlib')
depends_on('boost@1.55.0:')
depends_on('htslib@1.3.1:')
depends_on('doxygen+graphviz')
conflicts('%gcc@:5.2.0')
def cmake_args(self):
options = []
if self.run_tests:
options.append('-DPacBioBAM_build_tests:BOOL=ON')
else:
options.append('-DPacBioBAM_build_tests:BOOL=OFF')
return options
def install(self, spec, prefix):
install_tree('spack-build/bin', prefix.bin)
install_tree('spack-build/lib', prefix.lib)
install_tree('include/pbbam', prefix.include.pbbam)
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
spack_env.set('PacBioBAM_LIBRARIES', self.prefix.lib)
spack_env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include)