# 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 RAmpliqueso(RPackage):
    """Analysis of amplicon enrichment panels.

    The package provides tools and reports for the analysis of amplicon
    sequencing panels, such as AmpliSeq"""

    bioc = "ampliQueso"

    version("1.21.0", commit="ed99c5194a452ee299a93e981da2224e4dab5bdd")
    version("1.20.0", commit="ed064ffe9c5f2b47136e5f0f2e2c4214af4deae8")
    version("1.18.0", commit="c27fa51094135ef8da52cd2b34a27ec6454abd8e")
    version("1.16.0", commit="25d2543ff9dedef4f966f999c95cdf87185d3bb3")
    version("1.14.0", commit="9a4c26ec594171279aba8ab7fe59c4a2ea09b06b")

    depends_on("r+X", type=("build", "run"))
    depends_on("r@2.15.0:", type=("build", "run"))
    depends_on("r-rnaseqmap@2.17.1:", type=("build", "run"))
    depends_on("r-knitr", type=("build", "run"))
    depends_on("r-rgl", type=("build", "run"))
    depends_on("r-ggplot2", type=("build", "run"))
    depends_on("r-gplots", type=("build", "run"))
    depends_on("r-doparallel", type=("build", "run"))
    depends_on("r-foreach", type=("build", "run"))
    depends_on("r-variantannotation", type=("build", "run"))
    depends_on("r-genefilter", type=("build", "run"))
    depends_on("r-statmod", type=("build", "run"))
    depends_on("r-xtable", type=("build", "run"))
    depends_on("r-edger", type=("build", "run"))
    depends_on("r-deseq", type=("build", "run"))
    depends_on("r-samr", type=("build", "run"))