refactor: moving V-pipe specifics into module #62
Workflow file for this run
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| name: Docker Build and Test | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Cache Docker layers | |
| uses: actions/cache@v2 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx- | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - name: Install Docker Compose | |
| run: | | |
| sudo curl -L "https://github.com/docker/compose/releases/download/1.29.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose | |
| sudo chmod +x /usr/local/bin/docker-compose | |
| docker-compose --version | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Create .env file | |
| run: | | |
| echo SAMPLE_DIR=${{ secrets.SAMPLE_DIR }} >> .env | |
| echo SAMPLE_ID=${{ secrets.SAMPLE_ID }} >> .env | |
| echo BATCH_ID=${{ secrets.BATCH_ID }} >> .env | |
| echo TIMELINE_FILE=${{ secrets.TIMELINE_FILE }} >> .env | |
| echo PRIMER_FILE=${{ secrets.PRIMER_FILE }} >> .env | |
| echo NEXTCLADE_REFERENCE=${{ secrets.NEXTCLADE_REFERENCE }} >> .env | |
| echo RESULTS_DIR=${{ secrets.RESULTS_DIR }} >> .env | |
| echo AWS_ACCESS_KEY_ID=${{ secrets.AWS_ACCESS_KEY_ID }} >> .env | |
| echo AWS_SECRET_ACCESS_KEY=${{ secrets.AWS_SECRET_ACCESS_KEY }} >> .env | |
| echo AWS_DEFAULT_REGION=${{ secrets.AWS_DEFAULT_REGION }} >> .env | |
| - name: Build Docker image | |
| run: docker-compose --env-file .env build | |
| - name: Push to DockerHub | |
| if: github.ref == 'refs/heads/main' | |
| run: | | |
| docker-compose push | |
| test: | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Set up Docker Compose | |
| run: | | |
| sudo curl -L "https://github.com/docker/compose/releases/download/1.29.2/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose | |
| sudo chmod +x /usr/local/bin/docker-compose | |
| docker-compose --version | |
| - name: Create .env file | |
| run: | | |
| echo SAMPLE_DIR=${{ secrets.SAMPLE_DIR }} >> .env | |
| echo SAMPLE_ID=${{ secrets.SAMPLE_ID }} >> .env | |
| echo BATCH_ID=${{ secrets.BATCH_ID }} >> .env | |
| echo TIMELINE_FILE=${{ secrets.TIMELINE_FILE }} >> .env | |
| echo PRIMER_FILE=${{ secrets.PRIMER_FILE }} >> .env | |
| echo NEXTCLADE_REFERENCE=${{ secrets.NEXTCLADE_REFERENCE }} >> .env | |
| echo RESULTS_DIR=${{ secrets.RESULTS_DIR }} >> .env | |
| - name: Create Docker secrets files | |
| run: | | |
| mkdir -p ./secrets | |
| echo "${{ secrets.AWS_ACCESS_KEY_ID }}" > ./secrets/aws_access_key_id.txt | |
| echo "${{ secrets.AWS_SECRET_ACCESS_KEY }}" > ./secrets/aws_secret_access_key.txt | |
| echo "${{ secrets.AWS_DEFAULT_REGION }}" > ./secrets/aws_default_region.txt | |
| - name: Run Docker Compose | |
| run: docker-compose --env-file .env up | |
| - name: Tear down Docker Compose | |
| run: docker-compose down |