Include R #56
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| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - "*" | |
| pull_request: | |
| name: Quarto Publish | |
| jobs: | |
| build-deploy: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| with: | |
| tinytex: true | |
| - name: Install Python and Dependencies | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9' | |
| cache: 'pip' | |
| - run: pip install -r requirements.txt | |
| - 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 dependencies | |
| shell: Rscript {0} | |
| run: | | |
| BiocManager::install(c("knitr", "reticulate", "alabaster", "scRNAseq", "rmarkdown")) | |
| # - name: Install R | |
| # uses: r-lib/actions/setup-r@v2 | |
| # with: | |
| # r-version: 'devel' | |
| # - uses: r-lib/actions/setup-r-dependencies@v2 | |
| # with: | |
| # cache-version: 2 | |
| # packages: | | |
| # any::BiocManager | |
| # any::alabaster | |
| # any::scRNAseq | |
| # any::rmarkdown | |
| # any::knitr | |
| # any::reticulate | |
| # - run: Rscript r_requirements.r | |
| - name: Render | |
| uses: quarto-dev/quarto-actions/render@v2 | |
| with: | |
| to: html | |
| - name: Publish to GH Pages | |
| if: github.ref == 'refs/heads/master' | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| with: | |
| target: gh-pages # The branch the action should deploy to. | |
| render: false |