{% set version = "1.6.0" %}
{% set name = "scPipe" %}
{% set bioc = "3.9" %}

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: 7b3a3482d6610048fcdc9156f44610dd
build:
  number: 1
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: Rsubread, knitr, rmarkdown, testthat
requirements:
  host:
    - 'bioconductor-annotationdbi >=1.46.0,<1.47.0'
    - 'bioconductor-biocgenerics >=0.30.0,<0.31.0'
    - 'bioconductor-biomart >=2.40.0,<2.41.0'
    - 'bioconductor-genomicranges >=1.36.0,<1.37.0'
    - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0'
    - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0'
    - 'bioconductor-rhtslib >=1.16.0,<1.17.0'
    - 'bioconductor-rtracklayer >=1.44.0,<1.45.0'
    - 'bioconductor-s4vectors >=0.22.0,<0.23.0'
    - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0'
    - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0'
    - 'bioconductor-zlibbioc >=1.30.0,<1.31.0'
    - r-base
    - r-dplyr
    - r-ggally
    - r-ggplot2
    - r-glue
    - r-hashmap
    - r-magrittr
    - r-mass
    - r-mclust
    - 'r-rcpp >=0.11.3'
    - r-reshape
    - r-robustbase
    - r-scales
    - r-stringr
    - r-testthat
  run:
    - 'bioconductor-annotationdbi >=1.46.0,<1.47.0'
    - 'bioconductor-biocgenerics >=0.30.0,<0.31.0'
    - 'bioconductor-biomart >=2.40.0,<2.41.0'
    - 'bioconductor-genomicranges >=1.36.0,<1.37.0'
    - 'bioconductor-org.hs.eg.db >=3.8.0,<3.9.0'
    - 'bioconductor-org.mm.eg.db >=3.8.0,<3.9.0'
    - 'bioconductor-rhtslib >=1.16.0,<1.17.0'
    - 'bioconductor-rtracklayer >=1.44.0,<1.45.0'
    - 'bioconductor-s4vectors >=0.22.0,<0.23.0'
    - 'bioconductor-singlecellexperiment >=1.6.0,<1.7.0'
    - 'bioconductor-summarizedexperiment >=1.14.0,<1.15.0'
    - 'bioconductor-zlibbioc >=1.30.0,<1.31.0'
    - r-base
    - r-dplyr
    - r-ggally
    - r-ggplot2
    - r-glue
    - r-hashmap
    - r-magrittr
    - r-mass
    - r-mclust
    - 'r-rcpp >=0.11.3'
    - r-reshape
    - r-robustbase
    - r-scales
    - r-stringr
    - r-testthat
  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 preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.'
extra:
  parent_recipe:
    name: bioconductor-scpipe
    path: recipes/bioconductor-scpipe
    version: 1.2.1

