{% set version = "1.34.0" %}
{% set name = "GenomicAlignments" %}
{% 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://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ 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: ca8564f4590f770669cae948543cc9df
build:
  number: 1
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle
requirements:
  host:
    - 'bioconductor-biocgenerics >=0.44.0,<0.45.0'
    - 'bioconductor-biocparallel >=1.32.0,<1.33.0'
    - 'bioconductor-biostrings >=2.66.0,<2.67.0'
    - '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-rsamtools >=2.14.0,<2.15.0'
    - 'bioconductor-s4vectors >=0.36.0,<0.37.0'
    - 'bioconductor-summarizedexperiment >=1.28.0,<1.29.0'
    - r-base
    - libblas
    - liblapack
  run:
    - 'bioconductor-biocgenerics >=0.44.0,<0.45.0'
    - 'bioconductor-biocparallel >=1.32.0,<1.33.0'
    - 'bioconductor-biostrings >=2.66.0,<2.67.0'
    - '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-rsamtools >=2.14.0,<2.15.0'
    - 'bioconductor-s4vectors >=0.36.0,<0.37.0'
    - 'bioconductor-summarizedexperiment >=1.28.0,<1.29.0'
    - r-base
  build:
    - {{ compiler('c') }}
    - make
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: Artistic-2.0
  summary: 'Representation and manipulation of short genomic alignments'
  description: 'Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.'
extra:
  identifiers:
    - biotools:genomicalignments
  parent_recipe:
    name: bioconductor-genomicalignments
    path: recipes/bioconductor-genomicalignments
    version: 1.18.0