snakemake-run #376
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: '0 9 * * 5' | |
| name: snakemake-run | |
| jobs: | |
| snakemake-run: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| name: run snakemake | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-12, ubuntu-latest] | |
| include: | |
| - os: macos-12 | |
| rversion: '4.4' | |
| - os: ubuntu-latest | |
| rversion: '4.4' | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Install R (macOS) | |
| uses: r-lib/actions/setup-r@v2 | |
| if: runner.os == 'macOS' | |
| with: | |
| r-version: ${{ matrix.rversion }} | |
| - name: Check where R is installed | |
| if: runner.os == 'macOS' | |
| run: | | |
| which R | |
| Rscript -e 'print(.libPaths())' | |
| - name: Set up workflow R for macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| sed -i .bak 's/useCondaR: True/useCondaR: False/' config.yaml | |
| mkdir -p $HOME/Rlib | |
| echo "R_LIBS_USER=${HOME}/Rlib" > .Renviron | |
| cat .Renviron | |
| Rscript -e "install.packages('BiocManager'); BiocManager::install('GenomeInfoDbData')" | |
| - name: Set up conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: bioconda,conda-forge,nodefaults | |
| auto-activate-base: true | |
| miniforge-version: latest | |
| - name: Install system dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes | |
| sudo apt-get --yes --force-yes update -qq && \ | |
| sudo apt-get -y install libcairo2-dev libv8-dev \ | |
| libgdal-dev libgeos-dev libgeos++-dev libproj-dev libudunits2-dev \ | |
| libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libglpk-dev \ | |
| libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libgit2-dev \ | |
| libxml2-dev libuv1 libuv1-dev | |
| - name: Prepare for running workflow | |
| env: | |
| BIOCONDUCTOR_USE_CONTAINER_REPOSITORY: true | |
| run: | | |
| mkdir -p $HOME/.R | |
| echo -e 'MAKEFLAGS = -j8' > $HOME/.R/Makevars | |
| echo 'options(Ncpus = 8)' > $HOME/.Rprofile | |
| echo 'Sys.setenv(BIOCONDUCTOR_USE_CONTAINER_REPOSITORY=TRUE)' >> $HOME/.Rprofile | |
| - name: Install Snakemake | |
| run: | | |
| conda create -c conda-forge -c bioconda -n snakemake snakemake | |
| - name: Run Snakemake | |
| env: | |
| BIOCONDUCTOR_USE_CONTAINER_REPOSITORY: true | |
| run: | | |
| conda activate snakemake | |
| snakemake --use-conda --cores 4 | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: all_rout | |
| path: example_data/output/Rout/*.Rout |