typo #56
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| on: | |
| push: | |
| branches: | |
| - webpage | |
| - main | |
| workflow_dispatch: | |
| name: Quarto Publish | |
| jobs: | |
| build-deploy: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Install libcurl on Linux | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libglpk40 libglpk-dev | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - name: make work folder with data | |
| if: runner.os == 'Linux' | |
| run: sudo mkdir -p /work/Intro_to_bulkRNAseq/ | |
| - name: Get data | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo wget -O /work/Intro_to_bulkRNAseq/Data.zip https://zenodo.org/records/12090853/files/Data.zip?download=1 | |
| sudo unzip /work/Intro_to_bulkRNAseq/Data.zip -d /work/Intro_to_bulkRNAseq/ | |
| sudo rm /work/Intro_to_bulkRNAseq/Data.zip | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Check renv paths | |
| run: | | |
| Rscript -e 'cat("Project Library:", renv::paths$library(), "\n")' | |
| Rscript -e 'cat("Global Cache:", renv::paths$cache(), "\n")' | |
| - name: Set custom renv library path | |
| run: echo "RENV_PATHS_LIBRARY=~/renv/library/4.4.2/" >> $GITHUB_ENV | |
| - name: Install R Dependencies | |
| uses: r-lib/actions/setup-renv@v2 | |
| - name: Pull Notebooks folder content | |
| if: runner.os == 'Linux' | |
| run: | | |
| git clone https://github.com/hds-sandbox/bulk_RNAseq_course.git temp_repo | |
| cp -r temp_repo/Notebooks/*.Rmd develop | |
| cp -r temp_repo/Notebooks/img/* develop/img/ | |
| rm -rf temp_repo | |
| - name: Render and Publish | |
| uses: quarto-dev/quarto-actions/publish@v2 | |
| env: | |
| RENV_PATHS_LIBRARY: ~/renv/library/4.4.2/ | |
| with: | |
| target: gh-pages |