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# Copyright 2013-2024 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 Stacks(AutotoolsPackage):
"""Stacks is a software pipeline for building loci from short-read
sequences, such as those generated on the Illumina platform."""
homepage = "https://catchenlab.life.illinois.edu/stacks/"
url = "https://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz"
license("GPL-3.0-or-later")
version("2.53", sha256="ee1efceaeeeb7a39f0c2e804ad7c0a003094db28c9101120c38ddb02846e90fd")
version("2.3b", sha256="a46786d8811a730ebcdc17891e89f50d4f4ae196734439dac86091f45c92ac72")
version("1.46", sha256="45a0725483dc0c0856ad6b1f918e65d91c1f0fe7d8bf209f76b93f85c29ea28a")
variant("sparsehash", default=True, description="Improve Stacks memory usage with SparseHash")
depends_on("perl", type=("build", "run"))
depends_on("sparsehash", when="+sparsehash")
depends_on("zlib-api", when="@2.3b:")
conflicts("%gcc@:4.9.0", when="@2.3b:")
def configure_args(self):
args = []
if "+sparsehash" in self.spec:
args.append("--enable-sparsehash")
else:
args.append("--disable-sparsehash")
return args
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