clusterProfiler/.github/workflows/update_kegg_data.yml at devel · YuLab-SMU/clusterProfiler · GitHub

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name: Update KEGG Data

on:
  schedule:
    # Run at 00:00 on Sunday (UTC)
    - cron: '0 0 * * 0'
  workflow_dispatch:

jobs:
  update-data:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    permissions:
      contents: write

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          ref: devel

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Setup R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::rvest
            any::tibble
            any::tidyr
            any::devtools
            YuLab-SMU/yulab.utils
            YuLab-SMU/enrichit
            YuLab-SMU/enrichplot
            YuLab-SMU/GOSemSim
            YuLab-SMU/DOSE
            local::.
          needs: check

      - name: Install package
        run: |
          Rscript -e 'devtools::install()'

      - name: Update KEGG Data
        run: |
          Rscript -e 'source(system.file("extdata/kegg_pathway_category.r", package="clusterProfiler"))'
          Rscript -e 'clusterProfiler:::get_kegg_species(save=TRUE)'

          # Prepare staging directory
          mkdir -p staging
          cp data/kegg_category.rda staging/
          cp data/kegg_species.rda staging/

          # Generate md5.txt (Filename MD5)
          cd staging
          md5sum *.rda | awk '{print $2, $1}' > md5.txt
          cd ..
        shell: bash

      - name: Deploy to gh-pages
        uses: peaceiris/actions-gh-pages@v3
        with:
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: ./staging
          keep_files: true
          commit_message: "Deploy KEGG data"