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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
from spack.pkg.builtin.boost import Boost
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", sha256="45286e5f7deb7ff629e0643c8a416155915aec7b85d54c60b5cdc07f4d7b234a")
depends_on("zlib")
depends_on("boost@1.55.0:")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
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):
with working_dir(self.build_directory):
install_tree("bin", prefix.bin)
install_tree("lib", prefix.lib)
install_tree("pbbam", prefix.include.pbbam)
def setup_dependent_build_environment(self, env, dependent_spec):
env.set("PacBioBAM_LIBRARIES", self.prefix.lib)
env.set("PacBioBAM_INCLUDE_DIRS", self.prefix.include)
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