# 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 RRtracklayer(RPackage):
    """R interface to genome annotation files and the UCSC genome browser.

    Extensible framework for interacting with multiple genome browsers
    (currently UCSC built-in) and manipulating annotation tracks in various
    formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
    built-in). The user may export/import tracks to/from the supported
    browsers, as well as query and modify the browser state, such as the
    current viewport."""

    bioc = "rtracklayer"

    version("1.60.0", commit="de35bc03116fc7ad30f0e425b41715c3cb2e783b")
    version("1.58.0", commit="54a74972c08775fdf1e83e6e22cd0b8fad677fc1")
    version("1.56.1", commit="4c6d2201fcb102d471bd88f4f51cc34317669955")
    version("1.56.0", commit="1d70f7dc464ad87a1fde61588cd9ae0cb86b6e86")
    version("1.54.0", commit="04cdd75521a8364e67a49d7352500dd4a3e83c55")
    version("1.50.0", commit="d2e61f72ff5d5a94c2c487ba108a37f23bfcc1e6")
    version("1.44.4", commit="aec96e85daf53b5c5eb2e89250d2755352be4de3")
    version("1.42.2", commit="76702f671faea736807d54aeecfbadcd152d94c5")
    version("1.40.6", commit="ba9a6e711504a702147383bc7abfcc36eb304df7")
    version("1.38.3", commit="f20db703c09dc7e808c09e9b78c15aec9e546248")
    version("1.36.6", commit="8c0ac7230f94e0c5a981acbb178c8de70e968131")

    depends_on("r@3.3:", type=("build", "run"))
    depends_on("r-genomicranges@1.21.20:", type=("build", "run"))
    depends_on("r-genomicranges@1.37.2:", type=("build", "run"), when="@1.50.0:")
    depends_on("r-xml@1.98-0:", type=("build", "run"))
    depends_on("r-biocgenerics@0.13.8:", type=("build", "run"))
    depends_on("r-biocgenerics@0.25.1:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-biocgenerics@0.35.3:", type=("build", "run"), when="@1.50.0:")
    depends_on("r-s4vectors@0.13.13:", type=("build", "run"))
    depends_on("r-s4vectors@0.17.25:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-s4vectors@0.19.22:", type=("build", "run"), when="@1.42.2:")
    depends_on("r-s4vectors@0.23.18:", type=("build", "run"), when="@1.50.0:")
    depends_on("r-iranges@2.3.7:", type=("build", "run"))
    depends_on("r-iranges@2.11.12:", type=("build", "run"), when="@1.38.3:")
    depends_on("r-iranges@2.13.13:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-xvector@0.9.4:", type=("build", "run"))
    depends_on("r-xvector@0.19.7:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-genomeinfodb@1.3.14:", type=("build", "run"))
    depends_on("r-genomeinfodb@1.15.2:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-biostrings@2.43.7:", type=("build", "run"))
    depends_on("r-biostrings@2.47.6:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-zlibbioc", type=("build", "run"))
    depends_on("r-rcurl@1.4-2:", type=("build", "run"))
    depends_on("r-rsamtools@1.17.8:", type=("build", "run"))
    depends_on("r-rsamtools@1.31.2:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-genomicalignments@1.5.4:", type=("build", "run"))
    depends_on("r-genomicalignments@1.15.6:", type=("build", "run"), when="@1.40.6:")
    depends_on("r-biocio", type=("build", "run"), when="@1.54.0:")
    depends_on("r-restfulr@0.0.13:", type=("build", "run"), when="@1.54.0:")
    depends_on("zlib-api")
    depends_on("openssl")