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# Copyright 2013-2023 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 *
class Hal(MakefilePackage):
"""HAL is a structure to efficiently store and index multiple
genome alignments and ancestral reconstructions.
HAL is a graph-based representation which provides several advantages
over matrix/block-based formats such as MAF, such as
improved scalability and the ability to perform queries with
respect to an arbitrary reference or subtree."""
homepage = "https://github.com/ComparativeGenomicsToolkit/hal"
url = "https://github.com/ComparativeGenomicsToolkit/hal/archive/release-V2.1.tar.gz"
version("2.1", sha256="540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5")
maintainers("ilbiondo")
# HAL expects to be compiled alongside sonlib so we need both the
# source version and python library version
depends_on("hdf5+cxx~mpi")
depends_on("sonlib", type="build")
depends_on("python", type="run")
depends_on("py-sonlib", type="run")
# As we install sonlib seperately the include.mk needs
# editing to comment out an include
def patch(self):
includemk = FileFilter("include.mk")
includemk.filter(
r"^include \$\{sonLibRootDir\}/include\.mk", "# include ${sonLibRootDir}/include.mk"
)
def setup_build_environment(self, env):
env.set("sonLibRootDir", self.spec["sonlib"].prefix)
def install(self, spec, prefix):
# First the easy bit
install_tree("bin", prefix.bin)
install_tree("lib", prefix.lib)
# Copy the rest of the "toolkit" as to a directory named hal
# in order that the python libraries can be found and used
haldirs = [
"alignmentDepth",
"analysis",
"api",
"assemblyHub",
"benchmarks",
"blockViz",
"doc",
"extra",
"extract",
"fasta",
"liftover",
"lod",
"maf",
"modify",
"mutations",
"objs",
"phyloP",
"randgen",
"stats",
"synteny",
"testdata",
"validate",
]
for folder in haldirs:
install_tree(folder, join_path(self.prefix, "hal", folder))
install("__init__.py", join_path(self.prefix, "hal"))
# Now in order to make things useful we copy some python tools to bin
halpyfiles = [
"analysis/halContiguousRegions.py",
"assemblyHub/hal2assemblyHub.py",
"liftover/halLiftoverStatus.py",
"lod/halLodBenchmark.py",
"lod/halLodInterpolate.py",
"maf/hal2mafMP.py",
"phyloP/halPhyloPMP.py",
]
for pyfile in halpyfiles:
install(pyfile, self.prefix.bin)
# The hal directory is a python library so we set the path
# to be the installation root
def setup_run_environment(self, env):
env.prepend_path("PYTHONPATH", self.prefix)
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