{% set version = "2.20.0" %}
{% set name = "TCGAbiolinks" %}
{% set bioc = "3.13" %}

package:
  name: 'bioconductor-{{ name|lower }}'
  version: '{{ version }}'
source:
  url:
    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
  md5: 7188e985e16825ae18f487644c0b41a7
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
  noarch: generic
# Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid
requirements:
  host:
    - 'bioconductor-biomart >=2.48.0,<2.49.0'
    - 'bioconductor-genomicranges >=1.44.0,<1.45.0'
    - 'bioconductor-iranges >=2.26.0,<2.27.0'
    - 'bioconductor-s4vectors >=0.30.0,<0.31.0'
    - 'bioconductor-summarizedexperiment >=1.22.0,<1.23.0'
    - 'bioconductor-tcgabiolinksgui.data >=1.12.0,<1.13.0'
    - r-base
    - r-data.table
    - 'r-downloader >=0.4'
    - r-dplyr
    - r-ggplot2
    - 'r-httr >=1.2.1'
    - 'r-jsonlite >=1.0.0'
    - r-knitr
    - r-plyr
    - r-purrr
    - r-r.utils
    - r-readr
    - 'r-rvest >=0.3.0'
    - 'r-stringr >=1.0.0'
    - r-tibble
    - r-tidyr
    - 'r-xml >=3.98.0'
    - r-xml2
  run:
    - 'bioconductor-biomart >=2.48.0,<2.49.0'
    - 'bioconductor-genomicranges >=1.44.0,<1.45.0'
    - 'bioconductor-iranges >=2.26.0,<2.27.0'
    - 'bioconductor-s4vectors >=0.30.0,<0.31.0'
    - 'bioconductor-summarizedexperiment >=1.22.0,<1.23.0'
    - 'bioconductor-tcgabiolinksgui.data >=1.12.0,<1.13.0'
    - r-base
    - r-data.table
    - 'r-downloader >=0.4'
    - r-dplyr
    - r-ggplot2
    - 'r-httr >=1.2.1'
    - 'r-jsonlite >=1.0.0'
    - r-knitr
    - r-plyr
    - r-purrr
    - r-r.utils
    - r-readr
    - 'r-rvest >=0.3.0'
    - 'r-stringr >=1.0.0'
    - r-tibble
    - r-tidyr
    - 'r-xml >=3.98.0'
    - r-xml2
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: 'GPL (>= 3)'
  summary: 'TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data'
  description: 'The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.'
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
extra:
  identifiers:
    - biotools:tcgabiolinks
    - doi:10.1093/nar/gkv1507
  parent_recipe:
    name: bioconductor-tcgabiolinks
    path: recipes/bioconductor-tcgabiolinks
    version: 2.8.4

