{% set version = "1.12.0" %}
{% set name = "scPipe" %}
{% set bioc = "3.12" %}

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: c1c909da8ac4381a966cb545f110dbb1
build:
  number: 1
  rpaths:
    - lib/R/lib/
    - lib/
# Suggests: Rsubread, knitr, rmarkdown, testthat
# SystemRequirements: C++11, GNU make
requirements:
  host:
    - 'bioconductor-annotationdbi >=1.52.0,<1.53.0'
    - 'bioconductor-biocgenerics >=0.36.0,<0.37.0'
    - 'bioconductor-biomart >=2.46.0,<2.47.0'
    - 'bioconductor-genomicranges >=1.42.0,<1.43.0'
    - 'bioconductor-org.hs.eg.db >=3.12.0,<3.13.0'
    - 'bioconductor-org.mm.eg.db >=3.12.0,<3.13.0'
    - 'bioconductor-rhtslib >=1.22.0,<1.23.0'
    - 'bioconductor-rtracklayer >=1.50.0,<1.51.0'
    - 'bioconductor-s4vectors >=0.28.0,<0.29.0'
    - 'bioconductor-scater >=1.18.0,<1.19.0'
    - 'bioconductor-singlecellexperiment >=1.12.0,<1.13.0'
    - 'bioconductor-summarizedexperiment >=1.20.0,<1.21.0'
    - 'bioconductor-zlibbioc >=1.36.0,<1.37.0'
    - r-base
    - r-dplyr
    - r-ggally
    - r-ggplot2
    - 'r-glue >=1.3.0'
    - r-hash
    - r-magrittr
    - r-mass
    - r-mclust
    - 'r-rcpp >=0.11.3'
    - r-reshape
    - r-rlang
    - r-robustbase
    - r-scales
    - r-stringr
    - r-testthat
    - libblas
    - liblapack
  run:
    - 'bioconductor-annotationdbi >=1.52.0,<1.53.0'
    - 'bioconductor-biocgenerics >=0.36.0,<0.37.0'
    - 'bioconductor-biomart >=2.46.0,<2.47.0'
    - 'bioconductor-genomicranges >=1.42.0,<1.43.0'
    - 'bioconductor-org.hs.eg.db >=3.12.0,<3.13.0'
    - 'bioconductor-org.mm.eg.db >=3.12.0,<3.13.0'
    - 'bioconductor-rhtslib >=1.22.0,<1.23.0'
    - 'bioconductor-rtracklayer >=1.50.0,<1.51.0'
    - 'bioconductor-s4vectors >=0.28.0,<0.29.0'
    - 'bioconductor-scater >=1.18.0,<1.19.0'
    - 'bioconductor-singlecellexperiment >=1.12.0,<1.13.0'
    - 'bioconductor-summarizedexperiment >=1.20.0,<1.21.0'
    - 'bioconductor-zlibbioc >=1.36.0,<1.37.0'
    - r-base
    - r-dplyr
    - r-ggally
    - r-ggplot2
    - 'r-glue >=1.3.0'
    - r-hash
    - r-magrittr
    - r-mass
    - r-mclust
    - 'r-rcpp >=0.11.3'
    - r-reshape
    - r-rlang
    - 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: 'pipeline for single cell RNA-seq data analysis'
  description: '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.'
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
extra:
  parent_recipe:
    name: bioconductor-scpipe
    path: recipes/bioconductor-scpipe
    version: 1.2.1

