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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)
import os
from spack.package import *
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"
maintainers = ["robqiao"]
version("5.3.1", sha256="45a673255bfe7e29ed1f5bdb6410aa45cb6b907400d038c3da9daf1058b09156")
depends_on("pbbam")
depends_on("hdf5+cxx@1.8.12:1.8")
# 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@2.7:2.8", type="build")
@run_before("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)
@run_before("install")
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_build_environment(self, env, dependent_spec):
env.prepend_path("LD_LIBRARY_PATH", self.spec.prefix.hdf)
env.prepend_path("LD_LIBRARY_PATH", self.spec.prefix.alignment)
env.prepend_path("LD_LIBRARY_PATH", self.spec.prefix.pbdata)
def setup_run_environment(self, env):
env.prepend_path("LD_LIBRARY_PATH", self.spec["blasr-libcpp"].prefix.pbdata)
env.prepend_path("LD_LIBRARY_PATH", self.spec["blasr-libcpp"].prefix.alignment)
env.prepend_path("LD_LIBRARY_PATH", self.spec["blasr-libcpp"].prefix.hdf)
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