{% set version = "2.16.0" %}
{% set name = "STAN" %}
{% set bioc = "3.11" %}

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: 09577afa8d7438aa78fe9c4e0a58b69c
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: BiocStyle, gplots, knitr
requirements:
  host:
    - 'bioconductor-biocgenerics >=0.34.0,<0.35.0'
    - 'bioconductor-genomeinfodb >=1.24.0,<1.25.0'
    - 'bioconductor-genomicranges >=1.40.0,<1.41.0'
    - 'bioconductor-gviz >=1.32.0,<1.33.0'
    - 'bioconductor-iranges >=2.22.0,<2.23.0'
    - 'bioconductor-s4vectors >=0.26.0,<0.27.0'
    - r-base
    - r-poilog
    - r-rsolnp
    - libblas
    - liblapack
  run:
    - 'bioconductor-biocgenerics >=0.34.0,<0.35.0'
    - 'bioconductor-genomeinfodb >=1.24.0,<1.25.0'
    - 'bioconductor-genomicranges >=1.40.0,<1.41.0'
    - 'bioconductor-gviz >=1.32.0,<1.33.0'
    - 'bioconductor-iranges >=2.22.0,<2.23.0'
    - 'bioconductor-s4vectors >=0.26.0,<0.27.0'
    - r-base
    - r-poilog
    - r-rsolnp
  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: 'The Genomic STate ANnotation Package'
  description: 'Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. STAN (genomic STate ANnotation) implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data (e.g. continuous, discrete, binary). STAN de novo learns and annotates the genome into a given number of ''genomic states''. The ''genomic states'' may for instance reflect distinct genome-associated protein complexes (e.g. ''transcription states'') or describe recurring patterns of chromatin features (referred to as ''chromatin states''). Unlike other tools, STAN also allows for the integration of strand-specific (e.g. RNA) and non-strand-specific data (e.g. ChIP).'
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
extra:
  identifiers:
    - biotools:stan
  parent_recipe:
    name: bioconductor-stan
    path: recipes/bioconductor-stan
    version: 2.8.0

