# 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 Bedtools2(Package):
    """Collectively, the bedtools utilities are a swiss-army knife of
    tools for a wide-range of genomics analysis tasks. The most
    widely-used tools enable genome arithmetic: that is, set theory
    on the genome."""

    homepage = "https://github.com/arq5x/bedtools2"
    url = "https://github.com/arq5x/bedtools2/archive/v2.30.0.tar.gz"

    license("MIT")

    version("2.31.1", sha256="79a1ba318d309f4e74bfa74258b73ef578dccb1045e270998d7fe9da9f43a50e")
    version("2.31.0", sha256="183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec")
    version("2.30.0", sha256="c575861ec746322961cd15d8c0b532bb2a19333f1cf167bbff73230a7d67302f")
    version("2.29.2", sha256="bc2f36b5d4fc9890c69f607d54da873032628462e88c545dd633d2c787a544a5")
    version("2.27.1", sha256="edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112")
    version("2.27.0", sha256="e91390b567e577d337c15ca301e264b0355441f5ab90fa4f971622e3043e0ca0")
    version("2.26.0", sha256="15db784f60a11b104ccbc9f440282e5780e0522b8d55d359a8318a6b61897977")
    version("2.25.0", sha256="159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb")
    version("2.23.0", sha256="9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056")

    depends_on("zlib-api")
    depends_on("bzip2", when="@2.29:")
    depends_on("xz", when="@2.29:")
    depends_on("python", type="build")

    patch("bedtools-gcc13.patch", level=1, when="@2.27:2.31.0%gcc@13:")

    def install(self, spec, prefix):
        make("prefix=%s" % prefix, "install")