docs: updated variant ontology list file names and added comment unde… #9
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| # based onhttps://github.com/horosin/pages-deploy | |
| # and https://lucacozzuto.medium.com/automatic-reports-with-bookdown-and-github-actions-3c19498394aa | |
| # and https://stackoverflow.com/questions/76723921/install-a-github-r-package-for-a-github-action | |
| # and https://docs.github.com/en/actions/learn-github-actions/variables | |
| # and https://github.com/salimkayabasi/drawio-github-action-installation/blob/main/.github/workflows/drawio.yml | |
| name: github pages | |
| on: | |
| push: | |
| branches: | |
| - master | |
| paths: | |
| - 'documentation/**' | |
| - '.github/workflows/**' | |
| pull_request: | |
| paths: | |
| - 'documentation/**' | |
| - '.github/workflows/**' | |
| env: | |
| DRAWIO_DISABLE_UPDATE: true | |
| DISPLAY: :99.0 | |
| CONFIG_FILE: config.yml | |
| R_ENVIRONMENT: github | |
| jobs: | |
| bookdown: | |
| name: Render-Book | |
| runs-on: ubuntu-20.04 | |
| defaults: | |
| run: | |
| working-directory: ./documentation | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| rtools-version: '42' | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install TinyTeX | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| env: | |
| TINYTEX_INSTALLER: TinyTeX | |
| - name: Instaling librsvg2 | |
| timeout-minutes: 3 | |
| run: | | |
| sudo apt-get install librsvg2-bin | |
| - name: Instaling drawio | |
| timeout-minutes: 3 | |
| run: | | |
| Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 & | |
| sudo mkdir -p /run/user/1001 | |
| sudo chmod -R 777 /run/user/1001 | |
| sudo snap install drawio | |
| - name: Install packages | |
| run: Rscript -e 'install.packages(c("tidyverse", "rmarkdown", "bookdown", "config", "remotes", "webshot", "readr", "dplyr", "DT", "plotly", "knitr", "knitrdrawio", "config", "ggplot2", "ComplexUpset", "snakecase", "readxl", "shinyLP"))' | |
| - name: Install knitrdrawio | |
| run: Rscript -e 'remotes::install_url("https://github.com/rchaput/knitrdrawio/archive/refs/tags/v0.2.2.tar.gz")' | |
| - name: Install phantomjs | |
| run: Rscript -e 'webshot::install_phantomjs()' | |
| - name: Render Book | |
| run: Rscript -e 'bookdown::render_book("index.Rmd", "all")' | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: build | |
| path: ./documentation/build | |
| if-no-files-found: error | |
| checkout-and-deploy: | |
| runs-on: ubuntu-20.04 | |
| needs: bookdown | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| # Artifact name | |
| name: build | |
| # Destination path | |
| path: docs | |
| - name: Deploy to GitHub Pages | |
| uses: Cecilapp/GitHub-Pages-deploy@v3 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| build_dir: docs | |
| branch: gh-pages |