Add airway trancript quant + install tximeta #74
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| name: Render and Deploy | |
| on: | |
| push: | |
| pull_request: | |
| ## If you need to clear the cache, update the number inside cache-version as | |
| ## discussed at https://github.com/r-lib/actions/issues/86. | |
| env: | |
| cache-version: 1 | |
| jobs: | |
| render: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.2' | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Set up TinyTex | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| - name: Install X11 dependencies on MacOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install --cask xquartz | |
| - name: Install curl Headers | |
| if: runner.os == 'linux' | |
| run: sudo apt-get install libcurl4-openssl-dev | |
| - name: Install magick on Linux | |
| if: runner.os == 'linux' | |
| run: sudo apt-get -y install libmagick++-dev | |
| - name: Install libnetcdf-dev on Linux | |
| if: runner.os == 'linux' | |
| run: sudo apt-get -y install libnetcdf-dev | |
| - name: Set up renv | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| cache-version: ${{ env.cache-version }} | |
| - name: Session info | |
| run: | | |
| install.packages('sessioninfo') | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Render site | |
| run: | | |
| rmarkdown::render_site() | |
| shell: Rscript {0} | |
| - name: Deploy 🚀 | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| uses: JamesIves/[email protected] | |
| with: | |
| BRANCH: gh-pages | |
| FOLDER: _site | |
| - name: Upload LaTeX logs | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: latex-logs | |
| path: | | |
| *.log | |
| *.tex |