text: # Copyright 2013-2022 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 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."""
  
      homepage = "https://bioconductor.org/packages/YAPSA"
      git      = "https://git.bioconductor.org/packages/YAPSA.git"
  
      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:', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-genomicranges', type=('build', 'run'))
      depends_on('r-ggplot2', type=('build', 'run'))
      depends_on('r-limsolve', when='@1.16.0:', type=('build', 'run'))
      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', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-pmcmr', type=('build', 'run'))
      depends_on('r-ggbeeswarm', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-complexheatmap', type=('build', 'run'))
      depends_on('r-keggrest', type=('build', 'run'))
      depends_on('r-biostrings', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-bsgenome-hsapiens-ucsc-hg19', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-magrittr', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-pracma', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-dplyr', when='@1.16.0:', type=('build', 'run'))
      depends_on('r-lsei', when='@:1.10.0', type=('build', 'run'))
  