Add reference to European Variation Archive (EVA) for variant data #249
Workflow file for this run
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| # workflow for building and deploying a Jekyll site to GitHub Pages | |
| # based on https://github.com/actions/starter-workflows/blob/main/pages/jekyll.yml | |
| name: Deploy Jekyll site to Pages | |
| on: | |
| push: | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| type: boolean | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: false | |
| ## Use this job step to debug | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled && always() }} | |
| # with: | |
| # limit-access-to-actor: true | |
| # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| # Allow one concurrent deployment | |
| concurrency: | |
| group: "pages" | |
| cancel-in-progress: true | |
| jobs: | |
| # Build job | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| # Omit installation of packages in "test" group in Gemfile & prevent | |
| # `bundle exec` from checking for the existence of those packages in | |
| # the (generated) Gemfile.lock | |
| BUNDLE_WITHOUT: test | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Setup Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.2' # Not needed with a .ruby-version file | |
| bundler-cache: true # runs 'bundle install' and caches installed gems automatically | |
| cache-version: 0 # Increment this number if you need to re-download cached gems | |
| - name: Setup Pages | |
| id: pages | |
| uses: actions/configure-pages@v1 | |
| - run: bundle exec jekyll build --baseurl ${{ steps.pages.outputs.base_path }} # defaults output to '/_site' | |
| - uses: actions/setup-node@v3 | |
| with: | |
| node-version: 18 | |
| - run: make jbrowse | |
| - run: mv assets/js/jbrowse _site/assets/js | |
| # create artifact.tar from ./_site directory & upload as artifact named 'github-pages' | |
| - name: Upload Pages artifact | |
| uses: actions/upload-pages-artifact@v1 | |
| check-links: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: github-pages | |
| - run: tar -xf artifact.tar && rm artifact.tar | |
| - name: Setup Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '3.2' # Not needed with a .ruby-version file | |
| bundler-cache: true # runs 'bundle install' and caches installed gems automatically | |
| cache-version: 0 # Increment this number if you need to re-download cached gems | |
| - name: install htmlproofer | |
| # need ruby >= 3.1 for html-proofer 5.x | |
| run: gem install html-proofer -v 5.0.8 | |
| # Cache HTMLProofer external URL results for 30 days, but using actions/cache/restore | |
| # and actions/cache/save so cache can still be saved when failure is reported | |
| # https://github.com/gjtorikian/html-proofer/#caching-with-continuous-integration | |
| - uses: actions/cache/restore@v3 | |
| id: restore-cache-htmlproofer | |
| with: | |
| path: tmp/.htmlproofer | |
| key: ${{ runner.os }}-html-proofer | |
| - name: run htmlproofer | |
| run: | | |
| htmlproofer --allow-missing-href --ignore-missing-alt --ignore-files '/\/uikit\/tests\//' --ignore-status-codes '403,503' --cache '{"timeframe": {"external": "30d"}}' | |
| # https://github.com/actions/cache/blob/main/save/README.md#always-save-cache | |
| - uses: actions/cache/save@v3 | |
| id: save-cache-htmlproofer | |
| if: always() | |
| with: | |
| path: tmp/.htmlproofer | |
| key: ${{ runner.os }}-html-proofer | |
| # Deployment job | |
| deploy: | |
| if: ${{ github.ref == 'refs/heads/main' }} | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v1 |