edger.yaml 1.74 KB
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{
  id: edger,
  name: edgeR,
  article: "10.18129/B9.bioc.edgeR",
  website: "http://bioconductor.org/packages/release/bioc/html/edgeR.html",
  git: "git clone https://git.bioconductor.org/packages/edgeR",
  description: "Empirical Analysis of Digital Gene Expression Data.",
  commands:
    [
      {
        name: edger,
        command: ~,
        output_dir: edger,
        inputs: [{ name: counts }],
        outputs: [{ name: de_table }, { name: RData }],
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        options:
          [
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            {
              name: edger_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
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            {
              name: "edger_tx2gene",
              type: "checkbox",
              value: FALSE,
              label: "Aggregate transcripts counts to gene counts : ",
            },
            {
              name: "edger_annotations",
              type: "text",
              value: "",
              label: "Annotation file (gtf or gff) : ",
            },
          ],
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      },
    ],
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  version: "3.14.0",
  documentation: "http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf",
  install:
    {
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      limma: 'Rscript -e ''BiocManager::install("limma", version = "3.8",Ncpus=8)''',
      edger: 'Rscript -e ''BiocManager::install("edgeR", version = "3.8",Ncpus=8)''',
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      tximport: 'Rscript -e ''BiocManager::install("tximport", version = "3.8",Ncpus=8)''',
      rhdf5: 'Rscript -e ''BiocManager::install("rhdf5", version = "3.8",Ncpus=8)''',
      GenomicFeatures: 'Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.8",Ncpus=8)''',
    },
  script: edger.script.R,
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}