nanopore container splits #19
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| name: Build and publish pangolin docker image on push for tests | |
| on: [push] | |
| jobs: | |
| get-version: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Get current date | |
| id: date | |
| run: echo "::set-output name=date::$(date +'%Y-%m-%d')" | |
| - name: Test with environment variables | |
| run: echo $RELEASE_DATE | |
| env: | |
| RELEASE_DATE: ${{ steps.date.outputs.date }} | |
| - name: Fetch pangolin version | |
| shell: bash | |
| run: | | |
| ##Get pangolin-data version | |
| curl -sL https://api.github.com/repos/cov-lineages/pangolin-data/releases/latest | \ | |
| jq -r ".tag_name" > versions/pangolin-data-latest-version.txt | |
| pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt) | |
| echo $pangolin_data_VER | |
| ##Get constellations version | |
| curl -sL https://api.github.com/repos/cov-lineages/constellations/releases/latest | \ | |
| jq -r ".tag_name" > versions/constellations-latest-version.txt | |
| constellations_VER=$(cat versions/constellations-latest-version.txt) | |
| echo $constellations_VER | |
| ##Get pangolin version | |
| curl -sL https://api.github.com/repos/cov-lineages/pangolin/releases/latest | \ | |
| jq -r ".tag_name" > versions/pangolin-latest-version.txt | |
| PANGOLIN_VER=$(cat versions/pangolin-latest-version.txt) | |
| echo $PANGOLIN_VER | |
| ##Get scorpio version | |
| curl -sL https://api.github.com/repos/cov-lineages/scorpio/releases/latest | \ | |
| jq -r ".tag_name" > versions/scorpio-latest-version.txt | |
| scorpio_VER=$(cat versions/scorpio-latest-version.txt) | |
| echo $scorpio_VER | |
| - name: Check for modified files | |
| id: git-check | |
| run: echo ::set-output name=modified::$([ -z "`git status --porcelain`" ] && echo "false" || echo "true") | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - name: Set up Docker Buildx | |
| id: buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build new docker image | |
| shell: bash | |
| run: | | |
| echo ${{ steps.date.outputs.date }} | |
| REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||') | |
| pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||') | |
| scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||') | |
| constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||') | |
| #Build docker for pangolin-check for specific requirements | |
| docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin-stage:latest -t genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} --build-arg PANGOLIN_VER=v${REPO_VER} . | |
| - name: Push Docker image to DockerHub | |
| shell: bash | |
| run: | | |
| REPO_VER=$(cat versions/pangolin-latest-version.txt | sed 's|v||') | |
| pangolin_data_VER=$(cat versions/pangolin-data-latest-version.txt | sed 's|v||') | |
| scorpio_VER=$(cat versions/scorpio-latest-version.txt | sed 's|v||') | |
| constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||') | |
| #Push to dockerhub for pangolin with specific requirements | |
| docker image push genomicmedicinesweden/gms-artic-pangolin-stage:latest | |
| docker image push genomicmedicinesweden/gms-artic-pangolin-stage:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER} |