update tutorial #27
Workflow file for this run
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| name: Quarto Publish | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build-deploy: | |
| container: | |
| image: bioconductor/bioconductor_docker:devel | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Install rsync | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y rsync | |
| # - name: Install curl | |
| # run: | | |
| # sudo apt-get install libcurl4-openssl-dev | |
| # - name: Setup Quarto | |
| # uses: quarto-dev/quarto-actions/setup@v2 | |
| # with: | |
| # tinytex: true | |
| - name: Setup Quarto | |
| run: | | |
| wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.43/quarto-1.5.43-linux-amd64.deb && \ | |
| dpkg -i quarto-1.5.43-linux-amd64.deb && \ | |
| rm quarto-1.5.43-linux-amd64.deb | |
| - name: Setup tinytex | |
| run: quarto install tinytex | |
| # - name: Setup Python | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: '3.9' | |
| # cache: 'pip' | |
| - name: Install Python dependencies | |
| run: pip install -r requirements.txt | |
| # - name: Setup R | |
| # uses: r-lib/actions/setup-r@v2 | |
| # with: | |
| # r-version: '4.4.0' | |
| - name: Set directories | |
| run: | | |
| echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV | |
| - name: Restore the package directory | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_PKG_DIR }} | |
| key: check-packages | |
| - name: Install R packages | |
| run: Rscript rpackages.R | |
| # build SQLite from source, because I need 3.35<= | |
| - name: Download SQLite3 | |
| run: | | |
| wget https://www.sqlite.org/2024/sqlite-autoconf-3450300.tar.gz | |
| tar -xvf sqlite-autoconf-3450300.tar.gz | |
| - name: Install SQLite3 | |
| run: | | |
| cd sqlite-autoconf-3450300 | |
| ./configure | |
| make | |
| sudo make install | |
| export PATH="/usr/local/lib:$PATH" | |
| cd .. | |
| - name: Quarto render | |
| run: | | |
| quarto render --execute --to html --output-dir ./build | |
| env: | |
| LD_LIBRARY_PATH: /usr/local/lib | |
| - name: Create nojekyll | |
| run: touch ./build/.nojekyll | |
| - name: GH Pages Deployment | |
| if: github.ref == 'refs/heads/master' | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| branch: gh-pages # The branch the action should deploy to. | |
| folder: ./build | |
| clean: true # Automatically remove deleted files from the deploy branch |