test export compiler #84
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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 libboost-all-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: | | |
| wget -O Data.zip https://zenodo.org/records/12090853/files/Data.zip?download=1 | |
| unzip Data.zip | |
| rm Data.zip | |
| mkdir -p Results | |
| - 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: Install fgsea with C++14 compiler | |
| run: | | |
| # Set the C++14 compiler and flags for this session | |
| export CXX=g++-11 | |
| export CXXFLAGS="-std=c++14" | |
| # Verify which compiler is being used | |
| g++-11 --version | |
| echo "Using compiler: $CXX" | |
| echo "Using CXXFLAGS: $CXXFLAGS" | |
| # Print R's understanding of the compilation environment | |
| R -e 'Sys.getenv(c("CXX", "CXXFLAGS"))' | |
| # Install fgsea from Bioconductor | |
| R -e 'install.packages("BiocManager")' | |
| R -e 'BiocManager::install(c("fgsea"))' | |
| - name: installations | |
| run: | | |
| R -e 'install.packages(c("devtools", "tidyverse", "RColorBrewer", "pheatmap", "ggrepel", "cowplot"))' | |
| R -e 'devtools::install_github("stephenturner/annotables")' | |
| R -e 'BiocManager::install(c("DESeq2", "clusterProfiler", "DOSE", "org.Hs.eg.db", "pathview", "DEGreport", "tximport", "AnnotationHub", "ensembldb","apeglm","ggnewscale"))' | |
| R -e 'install.packages(c("rmarkdown", "markdown", "knitr"))' | |
| env: | |
| GITHUB_PAT: ${{ secrets.TOKEN }} | |
| - 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 | |
| with: | |
| target: gh-pages |