# 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 RSomaticsignatures(RPackage):
    """Somatic Signatures.

    The SomaticSignatures package identifies mutational signatures of single
    nucleotide variants (SNVs). It provides a infrastructure related to the
    methodology described in Nik-Zainal (2012, Cell), with flexibility in
    the matrix decomposition algorithms."""

    bioc = "SomaticSignatures"

    license("MIT")

    version("2.36.0", commit="26ce72c1fc771f711796eccee0a24c1070d33066")
    version("2.34.0", commit="249b1ef7cef3c94cfb96cc8aa2a16e00c2bd5d1f")
    version("2.32.0", commit="444d37661d147618f6830fd5de01a83ddf2a694d")
    version("2.30.0", commit="03f7ad707f6530fa7f62093f808884b6e83b0526")
    version("2.26.0", commit="9d4bed6e118ac76755ffb7abd058b09bac58a9d7")
    version("2.20.0", commit="dbedc30d92b600b3a17de596ebe38d15982c70c6")
    version("2.18.0", commit="facccd67eee5202fcbe6ad32e667546546e7ccff")
    version("2.16.0", commit="4ae348d9fa096c0ec307df95149991edf6044977")
    version("2.14.0", commit="b12d24f86e96a7c6a17cbbad21ca14fa3aa7c60f")
    version("2.12.1", commit="932298c6877d076004de5541cec85a14e819517a")

    depends_on("r@3.1.0:", type=("build", "run"))
    depends_on("r-variantannotation", type=("build", "run"))
    depends_on("r-genomicranges", type=("build", "run"))
    depends_on("r-nmf", type=("build", "run"))
    depends_on("r-s4vectors", type=("build", "run"))
    depends_on("r-iranges", type=("build", "run"))
    depends_on("r-genomeinfodb", type=("build", "run"))
    depends_on("r-biostrings", type=("build", "run"))
    depends_on("r-ggplot2", type=("build", "run"))
    depends_on("r-ggbio", type=("build", "run"))
    depends_on("r-reshape2", type=("build", "run"))
    depends_on("r-nmf", type=("build", "run"), when="@2.26.0:")
    depends_on("r-pcamethods", type=("build", "run"))
    depends_on("r-biobase", type=("build", "run"))
    depends_on("r-proxy", type=("build", "run"))