Change start of CWL/Shell tool lesson, to include docker #367
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| name: Website | |
| on: | |
| push: | |
| branches: gh-pages | |
| pull_request: [] | |
| jobs: | |
| build-website: | |
| if: ${{ !endsWith(github.repository, '/styles') }} | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Set up Ruby | |
| uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: '2.7' | |
| bundler-cache: true | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.x' | |
| - name: Install GitHub Pages, Bundler, and kramdown gems | |
| run: | | |
| gem install github-pages bundler kramdown | |
| - name: Install Python modules | |
| run: | | |
| python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests | |
| - name: Checkout the lesson | |
| uses: actions/checkout@master | |
| with: | |
| fetch-depth: 0 | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Look for R-markdown files | |
| id: check-rmd | |
| run: | | |
| echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT | |
| - name: Set up R | |
| if: steps.check-rmd.outputs.count != 0 | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| install-r: false | |
| r-version: 'release' | |
| - name: Install needed packages | |
| if: steps.check-rmd.outputs.count != 0 | |
| run: | | |
| install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr')) | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| if: steps.check-rmd.outputs.count != 0 | |
| run: | | |
| source('bin/dependencies.R') | |
| deps <- identify_dependencies() | |
| create_description(deps) | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: steps.check-rmd.outputs.count != 0 | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies for R packages | |
| if: steps.check-rmd.outputs.count != 0 | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")') | |
| - run: make site | |
| - run: make lesson-check | |
| if: always() | |
| - run: make lesson-check-all | |
| if: always() |