{% set version = "1.0.0" %}
{% set name = "CleanUpRNAseq" %}
{% set bioc = "3.20" %}

about:
  description: RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.
  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
  license: GPL-3
  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
  summary: Detect and Correct Genomic DNA Contamination in RNA-seq Data

build:
  noarch: generic
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
  run_exports: '{{ pin_subpackage("bioconductor-cleanuprnaseq", max_pin="x.x") }}'

package:
  name: bioconductor-{{ name|lower }}
  version: '{{ version }}'

# Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0)
requirements:

  host:
    - bioconductor-annotationfilter >=1.30.0,<1.31.0
    - bioconductor-biocgenerics >=0.52.0,<0.53.0
    - bioconductor-biostrings >=2.74.0,<2.75.0
    - bioconductor-bsgenome >=1.74.0,<1.75.0
    - bioconductor-deseq2 >=1.46.0,<1.47.0
    - bioconductor-edger >=4.4.0,<4.5.0
    - bioconductor-ensembldb >=2.30.0,<2.31.0
    - bioconductor-genomeinfodb >=1.42.0,<1.43.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-limma >=3.62.0,<3.63.0
    - bioconductor-qsmooth >=1.22.0,<1.23.0
    - bioconductor-rsamtools >=2.22.0,<2.23.0
    - bioconductor-rsubread >=2.20.0,<2.21.0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
    - bioconductor-tximport >=1.34.0,<1.35.0
    - r-base
    - r-ggplot2
    - r-ggrepel
    - r-kernsmooth
    - r-pheatmap
    - r-r6
    - r-rcolorbrewer
    - r-reshape2

  run:
    - bioconductor-annotationfilter >=1.30.0,<1.31.0
    - bioconductor-biocgenerics >=0.52.0,<0.53.0
    - bioconductor-biostrings >=2.74.0,<2.75.0
    - bioconductor-bsgenome >=1.74.0,<1.75.0
    - bioconductor-deseq2 >=1.46.0,<1.47.0
    - bioconductor-edger >=4.4.0,<4.5.0
    - bioconductor-ensembldb >=2.30.0,<2.31.0
    - bioconductor-genomeinfodb >=1.42.0,<1.43.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-limma >=3.62.0,<3.63.0
    - bioconductor-qsmooth >=1.22.0,<1.23.0
    - bioconductor-rsamtools >=2.22.0,<2.23.0
    - bioconductor-rsubread >=2.20.0,<2.21.0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
    - bioconductor-tximport >=1.34.0,<1.35.0
    - r-base
    - r-ggplot2
    - r-ggrepel
    - r-kernsmooth
    - r-pheatmap
    - r-r6
    - r-rcolorbrewer
    - r-reshape2

source:
  md5: 3fff7d3325a4839106824d215c6f1876
  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

test:
  commands:
    - $R -e "library('{{ name }}')"

