Add RNA-seq & mutation courses; update host #32
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| name: Deploy Courses to GitHub Pages | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tinytex: true | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libfreetype6-dev libpng-dev zlib1g-dev | |
| - name: Install R dependencies | |
| run: | | |
| install.packages(c( | |
| "rmarkdown", | |
| "knitr", | |
| "showtext", | |
| "tidyverse", | |
| "DT", | |
| "reticulate" | |
| )) | |
| shell: Rscript {0} | |
| - name: Render website | |
| run: | | |
| echo "Rendering website..." | |
| bash build.sh | |
| - name: Setup Pages | |
| uses: actions/configure-pages@v4 | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: ./_site | |
| deploy: | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| needs: build | |
| if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |