Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows #443
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| #------------------------------------------------------------------------------# | |
| name: Install | |
| #------------------------------------------------------------------------------# | |
| # Workflow conditions | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths: | |
| - '.github/workflows/install.yaml' | |
| - 'workflow/Snakefile' | |
| - 'workflow/rules/*.smk' | |
| - 'workflow/envs/*/*.yaml' | |
| pull_request: | |
| branches: | |
| - '*' | |
| release: | |
| types: [published] | |
| #------------------------------------------------------------------------------# | |
| jobs: | |
| #----------------------------------------------------------------------------# | |
| install_conda: | |
| name: Install with Conda | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| #------------------------------------------------------------------------# | |
| # Env setup | |
| - name: setup environment variables | |
| run: | | |
| echo "CONDA_ENVS_PATH=/home/runner/miniconda/envs:/usr/share/miniconda/envs" >> $GITHUB_ENV | |
| echo "CONDA_PKGS_DIRS=/home/runner/miniconda/pkgs" >> $GITHUB_ENV | |
| echo "FLOWDASH_BIO_USERNAME=${{ secrets.FLOWDASH_BIO_USERNAME }}" >> $GITHUB_ENV | |
| echo "FLOWDASH_BIO_PASSWORD=${{ secrets.FLOWDASH_BIO_PASSWORD }}" >> $GITHUB_ENV | |
| #------------------------------------------------------------------------# | |
| # Checkout Repository | |
| - name: checkout repo | |
| uses: actions/checkout@v2 | |
| #------------------------------------------------------------------------# | |
| # Setup conda with mamba | |
| - name: setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| mamba-version: "*" | |
| channels: conda-forge | |
| # Install conda environment | |
| - name: create conda env | |
| run: mamba env create -f workflow/envs/merge/environment.yaml | |
| # Install lsd2 | |
| #- name: install lsd2 | |
| # shell: bash -l {0} | |
| # run: | | |
| # wget https://github.com/tothuhien/lsd2/releases/download/v1.9.9/lsd2_unix ; | |
| # mv lsd2_unix /home/runner/miniconda/envs/plague-phylogeography/bin/lsd2 ; | |
| # conda activate plague-phylogeography ; | |
| # which lsd2 ; | |
| # lsd2 -h ; | |
| #------------------------------------------------------------------------# | |
| # run help | |
| - name: run help | |
| shell: bash -l {0} | |
| run: | | |
| conda activate plague-phylogeography; | |
| snakemake help --profile profiles/gh-actions --configfile results/config/snakemake.yaml ; | |
| #------------------------------------------------------------------------# | |
| #- name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| #----------------------------------------------------------------------------# | |
| install_docker: | |
| name: Install with Docker | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| #------------------------------------------------------------------------# | |
| - name: setup environment variables | |
| run: | | |
| echo "DOCKER_USERNAME=${{ secrets.DOCKERHUB_USERNAME }}" >> $GITHUB_ENV | |
| echo "DOCKER_PASSWORD=${{ secrets.DOCKERHUB_PASSWORD }}" >> $GITHUB_ENV | |
| echo "FLOWDASH_BIO_USERNAME=${{ secrets.FLOWDASH_BIO_USERNAME }}" >> $GITHUB_ENV | |
| echo "FLOWDASH_BIO_PASSWORD=${{ secrets.FLOWDASH_BIO_PASSWORD }}" >> $GITHUB_ENV | |
| #------------------------------------------------------------------------# | |
| # Checkout Repository | |
| - name: checkout repo | |
| uses: actions/checkout@v2 | |
| #------------------------------------------------------------------------# | |
| # pull docker image | |
| - name: docker pull | |
| run: docker pull ktmeaton/plague-phylogeography:dev | |
| #------------------------------------------------------------------------# | |
| # run help | |
| - name: run help | |
| run: docker run -e FLOWDASH_BIO_USERNAME=$FLOWDASH_BIO_USERNAME -e FLOWDASH_BIO_PASSWORD=$FLOWDASH_BIO_PASSWORD -v $PWD:/pipeline -w /pipeline ktmeaton/plague-phylogeography:dev snakemake help --profile profiles/gh-actions --configfile results/config/snakemake.yaml; |