{% set version = "1.24.0" %}
{% set name = "methylKit" %}
{% 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: b8bf98f842f90ab6e4759bf0711282e0
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager
# SystemRequirements: GNU make
requirements:
  host:
    - 'bioconductor-fastseg >=1.44.0,<1.45.0'
    - '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-qvalue >=2.30.0,<2.31.0'
    - 'bioconductor-rhtslib >=2.0.0,<2.1.0'
    - 'bioconductor-rsamtools >=2.14.0,<2.15.0'
    - 'bioconductor-rtracklayer >=1.58.0,<1.59.0'
    - 'bioconductor-s4vectors >=0.36.0,<0.37.0'
    - 'bioconductor-zlibbioc >=1.44.0,<1.45.0'
    - r-base
    - 'r-data.table >=1.9.6'
    - r-emdbook
    - r-gtools
    - r-kernsmooth
    - r-mclust
    - r-mgcv
    - r-r.utils
    - r-rcpp
    - libblas
    - liblapack
  run:
    - 'bioconductor-fastseg >=1.44.0,<1.45.0'
    - '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-qvalue >=2.30.0,<2.31.0'
    - 'bioconductor-rhtslib >=2.0.0,<2.1.0'
    - 'bioconductor-rsamtools >=2.14.0,<2.15.0'
    - 'bioconductor-rtracklayer >=1.58.0,<1.59.0'
    - 'bioconductor-s4vectors >=0.36.0,<0.37.0'
    - 'bioconductor-zlibbioc >=1.44.0,<1.45.0'
    - r-base
    - 'r-data.table >=1.9.6'
    - r-emdbook
    - r-gtools
    - r-kernsmooth
    - r-mclust
    - r-mgcv
    - r-r.utils
    - r-rcpp
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - make
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: Artistic-2.0
  summary: 'DNA methylation analysis from high-throughput bisulfite sequencing results'
  description: 'methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.'
extra:
  identifiers:
    - biotools:methylkit
  parent_recipe:
    name: bioconductor-methylkit
    path: recipes/bioconductor-methylkit
    version: 1.6.3

