{% set version = "1.20.0" %}
{% set name = "MADSEQ" %}
{% set bioc = "3.14" %}

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: 49c975fd97fab13c38036b35ed50fcb4
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
  noarch: generic
# Suggests: knitr
requirements:
  host:
    - 'bioconductor-biostrings >=2.62.0,<2.63.0'
    - 'bioconductor-bsgenome >=1.62.0,<1.63.0'
    - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0'
    - 'bioconductor-genomeinfodb >=1.30.0,<1.31.0'
    - 'bioconductor-genomicalignments >=1.30.0,<1.31.0'
    - 'bioconductor-genomicranges >=1.46.0,<1.47.0'
    - 'bioconductor-iranges >=2.28.0,<2.29.0'
    - 'bioconductor-preprocesscore >=1.56.0,<1.57.0'
    - 'bioconductor-rsamtools >=2.10.0,<2.11.0'
    - 'bioconductor-rtracklayer >=1.54.0,<1.55.0'
    - 'bioconductor-s4vectors >=0.32.0,<0.33.0'
    - 'bioconductor-summarizedexperiment >=1.24.0,<1.25.0'
    - 'bioconductor-variantannotation >=1.40.0,<1.41.0'
    - 'bioconductor-zlibbioc >=1.40.0,<1.41.0'
    - r-base
    - r-coda
    - 'r-rjags >=4-6'
    - r-vcfr
    - r-vgam
  run:
    - 'bioconductor-biostrings >=2.62.0,<2.63.0'
    - 'bioconductor-bsgenome >=1.62.0,<1.63.0'
    - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0'
    - 'bioconductor-genomeinfodb >=1.30.0,<1.31.0'
    - 'bioconductor-genomicalignments >=1.30.0,<1.31.0'
    - 'bioconductor-genomicranges >=1.46.0,<1.47.0'
    - 'bioconductor-iranges >=2.28.0,<2.29.0'
    - 'bioconductor-preprocesscore >=1.56.0,<1.57.0'
    - 'bioconductor-rsamtools >=2.10.0,<2.11.0'
    - 'bioconductor-rtracklayer >=1.54.0,<1.55.0'
    - 'bioconductor-s4vectors >=0.32.0,<0.33.0'
    - 'bioconductor-summarizedexperiment >=1.24.0,<1.25.0'
    - 'bioconductor-variantannotation >=1.40.0,<1.41.0'
    - 'bioconductor-zlibbioc >=1.40.0,<1.41.0'
    - r-base
    - r-coda
    - 'r-rjags >=4-6'
    - r-vcfr
    - r-vgam
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: GPL(>=2)
  summary: 'Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data'
  description: 'The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.'
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
extra:
  identifiers:
    - biotools:madseq
    - doi:10.1101/142299
  parent_recipe:
    name: bioconductor-madseq
    path: recipes/bioconductor-madseq
    version: 1.6.1

