{% set version = "1.20.0" %}
{% set name = "IsoformSwitchAnalyzeR" %}
{% set bioc = "3.16" %}

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: 2efe2bf8079453afa4e6e8a84ee737fd
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown
requirements:
  host:
    - 'bioconductor-biobase >=2.58.0,<2.59.0'
    - 'bioconductor-biocgenerics >=0.44.0,<0.45.0'
    - 'bioconductor-biostrings >=2.66.0,<2.67.0'
    - 'bioconductor-bsgenome >=1.66.0,<1.67.0'
    - 'bioconductor-dexseq >=1.44.0,<1.45.0'
    - 'bioconductor-drimseq >=1.26.0,<1.27.0'
    - 'bioconductor-edger >=3.40.0,<3.41.0'
    - 'bioconductor-genomeinfodb >=1.34.0,<1.35.0'
    - 'bioconductor-genomicranges >=1.50.0,<1.51.0'
    - 'bioconductor-iranges >=2.32.0,<2.33.0'
    - 'bioconductor-limma >=3.54.0,<3.55.0'
    - 'bioconductor-rtracklayer >=1.58.0,<1.59.0'
    - 'bioconductor-tximeta >=1.16.0,<1.17.0'
    - 'bioconductor-tximport >=1.26.0,<1.27.0'
    - 'bioconductor-xvector >=0.38.0,<0.39.0'
    - r-base
    - r-dbi
    - r-dplyr
    - r-futile.logger
    - r-ggplot2
    - r-gridextra
    - r-magrittr
    - r-plyr
    - r-rcolorbrewer
    - r-rcurl
    - r-readr
    - r-reshape2
    - r-stringr
    - r-tibble
    - r-venndiagram
    - libblas
    - liblapack
  run:
    - 'bioconductor-biobase >=2.58.0,<2.59.0'
    - 'bioconductor-biocgenerics >=0.44.0,<0.45.0'
    - 'bioconductor-biostrings >=2.66.0,<2.67.0'
    - 'bioconductor-bsgenome >=1.66.0,<1.67.0'
    - 'bioconductor-dexseq >=1.44.0,<1.45.0'
    - 'bioconductor-drimseq >=1.26.0,<1.27.0'
    - 'bioconductor-edger >=3.40.0,<3.41.0'
    - 'bioconductor-genomeinfodb >=1.34.0,<1.35.0'
    - 'bioconductor-genomicranges >=1.50.0,<1.51.0'
    - 'bioconductor-iranges >=2.32.0,<2.33.0'
    - 'bioconductor-limma >=3.54.0,<3.55.0'
    - 'bioconductor-rtracklayer >=1.58.0,<1.59.0'
    - 'bioconductor-tximeta >=1.16.0,<1.17.0'
    - 'bioconductor-tximport >=1.26.0,<1.27.0'
    - 'bioconductor-xvector >=0.38.0,<0.39.0'
    - r-base
    - r-dbi
    - r-dplyr
    - r-futile.logger
    - r-ggplot2
    - r-gridextra
    - r-magrittr
    - r-plyr
    - r-rcolorbrewer
    - r-rcurl
    - r-readr
    - r-reshape2
    - r-stringr
    - r-tibble
    - r-venndiagram
  build:
    - {{ compiler('c') }}
    - make
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: 'GPL (>= 2)'
  summary: 'Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.'
  description: 'Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.'
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
extra:
  identifiers:
    - biotools:IsoformSwitchAnalyzeR
    - doi:10.1158/1541-7786.MCR-16-0459
  parent_recipe:
    name: bioconductor-isoformswitchanalyzer
    path: recipes/bioconductor-isoformswitchanalyzer
    version: 1.2.0

