snakemake-run #372
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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 |