# 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 RYapsa(RPackage):
    """Yet Another Package for Signature Analysis.

    This package provides functions and routines useful in the analysis of
    somatic signatures (cf. L. Alexandrov et al., Nature 2013). In
    particular, functions to perform a signature analysis with known
    signatures (LCD = linear combination decomposition) and a signature
    analysis on stratified mutational catalogue (SMC = stratify mutational
    catalogue) are provided."""

    bioc = "YAPSA"

    license("GPL-3.0-or-later")

    version("1.26.0", commit="eab6bbd7a44e1368c7827e4717439de445303868")
    version("1.24.0", commit="68d1c9c71af3ade4a44237ec2d3003688378f898")
    version("1.22.0", commit="55c2886874f154c737264ce6843089bf3565fa57")
    version("1.20.1", commit="6c3f437911859df6f6e4a9af5571c3a5aafbffb2")
    version("1.16.0", commit="f344cdb81bb886c633f9325f811912fb59d58eb1")
    version("1.10.0", commit="06af18e424868eb0f0be6c80e90cbab1eabf3d73")
    version("1.8.0", commit="402f3f7774fdf8afc7883579ad651c26df0f8fdb")
    version("1.6.0", commit="2455d272b076835ddb36ad21c01ef15af66abc36")
    version("1.4.0", commit="6f24150a0689d5215983975ece96c8c205923c72")
    version("1.2.0", commit="320809b69e470e30a777a383f8341f93064ec24d")

    depends_on("r@3.3.0:", type=("build", "run"))
    depends_on("r@3.6.0:", type=("build", "run"), when="@1.16.0:")
    depends_on("r-genomicranges", type=("build", "run"))
    depends_on("r-ggplot2", type=("build", "run"))
    depends_on("r-limsolve", type=("build", "run"), when="@1.16.0:")
    depends_on("r-somaticsignatures", type=("build", "run"))
    depends_on("r-variantannotation", type=("build", "run"))
    depends_on("r-genomeinfodb", type=("build", "run"))
    depends_on("r-reshape2", type=("build", "run"))
    depends_on("r-gridextra", type=("build", "run"))
    depends_on("r-corrplot", type=("build", "run"))
    depends_on("r-dendextend", type=("build", "run"))
    depends_on("r-getoptlong", type=("build", "run"))
    depends_on("r-circlize", type=("build", "run"))
    depends_on("r-gtrellis", type=("build", "run"))
    depends_on("r-doparallel", type=("build", "run"), when="@1.16.0:")
    depends_on("r-pmcmrplus", type=("build", "run"), when="@1.20.1:")
    depends_on("r-ggbeeswarm", type=("build", "run"), when="@1.16.0:")
    depends_on("r-complexheatmap", type=("build", "run"))
    depends_on("r-keggrest", type=("build", "run"))
    depends_on("r-biostrings", type=("build", "run"), when="@1.16.0:")
    depends_on("r-bsgenome-hsapiens-ucsc-hg19", type=("build", "run"), when="@1.16.0:")
    depends_on("r-magrittr", type=("build", "run"), when="@1.16.0:")
    depends_on("r-pracma", type=("build", "run"), when="@1.16.0:")
    depends_on("r-dplyr", type=("build", "run"), when="@1.16.0:")

    depends_on("r-lsei", type=("build", "run"), when="@:1.10.0")
    depends_on("r-pmcmr", type=("build", "run"), when="@:1.16.0")