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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 Odgi(CMakePackage):
"""Optimized dynamic genome/graph implementation.
Odgi provides an efficient and succinct dynamic DNA sequence graph model, as
well as a host of algorithms that allow the use of such graphs in
bioinformatic analyses.
"""
homepage = "https://github.com/pangenome/odgi"
git = "https://github.com/pangenome/odgi.git"
# notify when the package is updated.
maintainers("tbhaxor", "EbiArnie")
# <<< Versions list starts here
version("0.8.3", commit="34f006f31c3f6b35a1eb8d58a4edb1c458583de3", submodules=True)
# >>> Versions list ends here
# compilation problem with ninja
generator("make", default="make")
# the range is required to successfully build the program
requires("%gcc", msg="Package odgi depends on the gcc C++ compiler")
conflicts(
"%gcc@:9.2,13:", msg="Unsupported compiler version. Recommended range is 9.3 -> 12.x"
)
# <<< Dependencies list starts here
depends_on("python")
depends_on("py-pybind11")
depends_on("sdsl-lite")
depends_on("libdivsufsort")
depends_on("jemalloc")
# >>> Dependencies list ends here
def cmake_args(self):
args = [
"-DCMAKE_CXX_STANDARD_REQUIRED:BOOL=ON",
"-DPYTHON_EXECUTABLE:FILEPATH={0}".format(self.spec["python"].command),
]
return args
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