snakemake-run #282
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| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: '0 9 * * 5' | |
| name: snakemake-run | |
| jobs: | |
| snakemake-run: | |
| name: run snakemake | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| include: | |
| - os: macos-latest | |
| rversion: '4.2' | |
| - os: ubuntu-latest | |
| rversion: '4.2' | |
| 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: s-weigand/[email protected] | |
| with: | |
| activate-conda: true | |
| update-conda: true | |
| conda-channels: 'bioconda,conda-forge,defaults' | |
| - 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 | |
| - name: Install snakemake (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| conda install -c conda-forge mamba=0.23.3 | |
| rm -f /usr/share/miniconda/pkgs/cache/*.json # workaround from mamba-org/mamba#488 | |
| mamba install -c bioconda snakemake=6.10.0 | |
| - name: Install snakemake (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| conda install -c conda-forge mamba=0.23.3 | |
| mamba install -c bioconda snakemake=6.10.0 | |
| - name: Run 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 | |
| snakemake --use-conda --cores 4 --conda-frontend mamba | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v2 | |
| if: failure() | |
| with: | |
| name: all_rout | |
| path: example_data/output/Rout/*.Rout |