{% set version = "1.44.0" %}
{% set name = "ShortRead" %}
{% set bioc = "3.10" %}

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: 68a4816003752d9ebfdeb0ff0c892fe6
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
requirements:
  host:
    - 'bioconductor-biobase >=2.46.0,<2.47.0'
    - 'bioconductor-biocgenerics >=0.32.0,<0.33.0'
    - 'bioconductor-biocparallel >=1.20.0,<1.21.0'
    - 'bioconductor-biostrings >=2.54.0,<2.55.0'
    - 'bioconductor-genomeinfodb >=1.22.0,<1.23.0'
    - 'bioconductor-genomicalignments >=1.22.0,<1.23.0'
    - 'bioconductor-genomicranges >=1.38.0,<1.39.0'
    - 'bioconductor-iranges >=2.20.0,<2.21.0'
    - 'bioconductor-rsamtools >=2.2.0,<2.3.0'
    - 'bioconductor-s4vectors >=0.24.0,<0.25.0'
    - 'bioconductor-xvector >=0.26.0,<0.27.0'
    - 'bioconductor-zlibbioc >=1.32.0,<1.33.0'
    - r-base
    - r-hwriter
    - r-lattice
    - r-latticeextra
  run:
    - 'bioconductor-biobase >=2.46.0,<2.47.0'
    - 'bioconductor-biocgenerics >=0.32.0,<0.33.0'
    - 'bioconductor-biocparallel >=1.20.0,<1.21.0'
    - 'bioconductor-biostrings >=2.54.0,<2.55.0'
    - 'bioconductor-genomeinfodb >=1.22.0,<1.23.0'
    - 'bioconductor-genomicalignments >=1.22.0,<1.23.0'
    - 'bioconductor-genomicranges >=1.38.0,<1.39.0'
    - 'bioconductor-iranges >=2.20.0,<2.21.0'
    - 'bioconductor-rsamtools >=2.2.0,<2.3.0'
    - 'bioconductor-s4vectors >=0.24.0,<0.25.0'
    - 'bioconductor-xvector >=0.26.0,<0.27.0'
    - 'bioconductor-zlibbioc >=1.32.0,<1.33.0'
    - r-base
    - r-hwriter
    - r-lattice
    - r-latticeextra
  build:
    - {{ compiler('c') }}
    - {{ compiler('cxx') }}
    - automake
    - make
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: Artistic-2.0
  summary: 'FASTQ input and manipulation'
  description: 'This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes.  The package also contains legacy support for early single-end, ungapped alignment formats.'
extra:
  identifiers:
    - biotools:shortread
  parent_recipe:
    name: bioconductor-shortread
    path: recipes/bioconductor-shortread
    version: 1.38.0

