{% set version = "2.11.0" %}
{% set name = "GenoGAM" %}
{% 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: b557796689a0ac7dd58a276af43aa642
build:
  number: 1
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown
requirements:
  host:
    - 'bioconductor-biocparallel >=1.28.0,<1.29.0'
    - 'bioconductor-biostrings >=2.62.0,<2.63.0'
    - 'bioconductor-delayedarray >=0.20.0,<0.21.0'
    - 'bioconductor-deseq2 >=1.34.0,<1.35.0'
    - '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-hdf5array >=1.22.0,<1.23.0'
    - 'bioconductor-iranges >=2.28.0,<2.29.0'
    - 'bioconductor-rhdf5 >=2.38.0,<2.39.0'
    - 'bioconductor-rsamtools >=2.10.0,<2.11.0'
    - 'bioconductor-s4vectors >=0.32.0,<0.33.0'
    - 'bioconductor-summarizedexperiment >=1.24.0,<1.25.0'
    - r-base
    - 'r-data.table >=1.9.4'
    - 'r-futile.logger >=1.4.1'
    - 'r-matrix >=1.2-8'
    - 'r-rcpp >=0.12.14'
    - r-rcpparmadillo
    - 'r-sparseinv >=0.1.1'
    - libblas
    - liblapack
  run:
    - 'bioconductor-biocparallel >=1.28.0,<1.29.0'
    - 'bioconductor-biostrings >=2.62.0,<2.63.0'
    - 'bioconductor-delayedarray >=0.20.0,<0.21.0'
    - 'bioconductor-deseq2 >=1.34.0,<1.35.0'
    - '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-hdf5array >=1.22.0,<1.23.0'
    - 'bioconductor-iranges >=2.28.0,<2.29.0'
    - 'bioconductor-rhdf5 >=2.38.0,<2.39.0'
    - 'bioconductor-rsamtools >=2.10.0,<2.11.0'
    - 'bioconductor-s4vectors >=0.32.0,<0.33.0'
    - 'bioconductor-summarizedexperiment >=1.24.0,<1.25.0'
    - r-base
    - 'r-data.table >=1.9.4'
    - 'r-futile.logger >=1.4.1'
    - 'r-matrix >=1.2-8'
    - 'r-rcpp >=0.12.14'
    - r-rcpparmadillo
    - 'r-sparseinv >=0.1.1'
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - make
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: GPL-2
  summary: 'A GAM based framework for analysis of ChIP-Seq data'
  description: 'This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package ''mgcv''. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.'
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
extra:
  identifiers:
    - biotools:genogam
    - doi:10.1093/bioinformatics/btx150
  parent_recipe:
    name: bioconductor-genogam
    path: recipes/bioconductor-genogam
    version: 1.8.0

