add htlib dependencies #8
Workflow file for this run
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| name: Render R Markdown | ||
| on: | ||
| push: | ||
| branches: [main] | ||
| pull_request: | ||
| branches: [main] | ||
| jobs: | ||
| render-rmd: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
| - name: Install pandoc | ||
| uses: pandoc/actions/setup@v1 | ||
| - name: Run pandoc | ||
| run: pandoc --version | ||
| - name: Setup R | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
| # Cache R package installations | ||
| - name: Cache R packages | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ~/.R/ | ||
| key: ${{ runner.os }}-R-${{ hashFiles('**/*.Rmd', '**/*.R') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-R- | ||
| - name: Install system dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y libcurl4-openssl-dev libfontconfig1-dev libfreetype6-dev | ||
| - name: Install necessary R packages | ||
| run: | | ||
| R -e 'install.packages("BiocManager")' | ||
| R -e 'BiocManager::install("renv")' | ||
| R -e 'BiocManager::install(c("Rhtslib", "Rsamtools", "GenomicAlignments", "rtracklayer", "systemfonts"))' | ||
| R -e 'BiocManager::install(renv::dependencies(path = "./01_quality_assessment/.")[["Package"]])' | ||
| # Add any other package installations you need here | ||
| # e.g., Rscript ./install_depedencies.R | ||
| - name: Render R Markdown | ||
| run: | | ||
| Rscript -e 'rmarkdown::render("./01_quality_assessment/QC.Rmd")' | ||
| - name: Upload HTML report | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: rendered-report | ||
| path: ./01_quality_assessment/QC.html | ||
