working docker setup #158
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| name: Snakemake | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| jobs: | |
| run_snakemake: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # Required when using an activated conda environment in steps | |
| # See https://github.com/conda-incubator/setup-miniconda#IMPORTANT | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| python: ['3.10'] | |
| fail-fast: false | |
| services: | |
| postgres: | |
| image: postgres | |
| env: | |
| POSTGRES_USER: scott | |
| POSTGRES_PASSWORD: tiger | |
| POSTGRES_DB: guidescan | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # Maps tcp port 5432 on service container to the host | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install essentials | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y build-essential | |
| - name: Set up conda environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python }} | |
| - name: Install pip | |
| run: conda install pip | |
| - name: Install package | |
| run: pip install .[dev] | |
| - name: Install guidescan | |
| run: conda install -c conda-forge -c bioconda guidescan | |
| - name: Pytest in Snakemake (default sqlite) | |
| run: | | |
| cd docker/snakemake | |
| snakemake -F guidescan_pytest --cores 1 --use-conda --config max_kmers=1000 enzymes="[\"cas9\"]" organisms="[\"sacCer3\"]" --conda-frontend conda | |
| - name: Pytest in Snakemake (postgres) | |
| run: | | |
| cd docker/snakemake | |
| snakemake -F guidescan_pytest --cores 1 --use-conda --config max_kmers=1000 enzymes="[\"cas9\"]" organisms="[\"sacCer3\"]" --conda-frontend conda | |
| env: | |
| GUIDESCAN_GUIDESCAN_DB: postgresql+psycopg2://scott:tiger@localhost/guidescan |