603569e321
* Style: black 23, skip magic trailing commas * isort should use same line length as black * Fix unused import * Update version of black used in CI * Update new packages * Update new packages
105 lines
3.2 KiB
Python
105 lines
3.2 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Hal(MakefilePackage):
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"""HAL is a structure to efficiently store and index multiple
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genome alignments and ancestral reconstructions.
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HAL is a graph-based representation which provides several advantages
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over matrix/block-based formats such as MAF, such as
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improved scalability and the ability to perform queries with
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respect to an arbitrary reference or subtree."""
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homepage = "https://github.com/ComparativeGenomicsToolkit/hal"
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url = "https://github.com/ComparativeGenomicsToolkit/hal/archive/release-V2.1.tar.gz"
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version("2.1", "540255be1af55abf390359fe034b82d7e61bdf6c3277df3cc01259cd450994e5")
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maintainers("ilbiondo")
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# HAL expects to be compiled alongside sonlib so we need both the
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# source version and python library version
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depends_on("hdf5+cxx~mpi")
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depends_on("sonlib", type="build")
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depends_on("python", type="run")
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depends_on("py-sonlib", type="run")
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# As we install sonlib seperately the include.mk needs
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# editing to comment out an include
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def patch(self):
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includemk = FileFilter("include.mk")
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includemk.filter(
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r"^include \$\{sonLibRootDir\}/include\.mk", "# include ${sonLibRootDir}/include.mk"
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)
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def setup_build_environment(self, env):
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env.set("sonLibRootDir", self.spec["sonlib"].prefix)
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def install(self, spec, prefix):
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# First the easy bit
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install_tree("bin", prefix.bin)
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install_tree("lib", prefix.lib)
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# Copy the rest of the "toolkit" as to a directory named hal
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# in order that the python libraries can be found and used
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haldirs = [
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"alignmentDepth",
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"analysis",
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"api",
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"assemblyHub",
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"benchmarks",
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"blockViz",
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"doc",
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"extra",
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"extract",
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"fasta",
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"liftover",
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"lod",
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"maf",
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"modify",
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"mutations",
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"objs",
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"phyloP",
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"randgen",
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"stats",
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"synteny",
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"testdata",
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"validate",
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]
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for folder in haldirs:
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install_tree(folder, join_path(self.prefix, "hal", folder))
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install("__init__.py", join_path(self.prefix, "hal"))
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# Now in order to make things useful we copy some python tools to bin
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halpyfiles = [
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"analysis/halContiguousRegions.py",
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"assemblyHub/hal2assemblyHub.py",
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"liftover/halLiftoverStatus.py",
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"lod/halLodBenchmark.py",
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"lod/halLodInterpolate.py",
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"maf/hal2mafMP.py",
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"phyloP/halPhyloPMP.py",
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]
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for pyfile in halpyfiles:
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install(pyfile, self.prefix.bin)
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# The hal directory is a python library so we set the path
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# to be the installation root
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def setup_run_environment(self, env):
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env.prepend_path("PYTHONPATH", self.prefix)
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