build_dockerfile_pangolin_master.yml

name: Build and publish pangolin docker image for master

on:
 schedule:
   - cron: '0 0 * * *'
 push:
    branches:
      - master

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=$(cat versions/constellations-latest-version.txt | sed 's|v||')
         #Build docker for pangolin-check for specific requirements
         docker build --no-cache -f environments/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ 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:latest
         docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-d-${pangolin_data_VER}-c-${constellations_VER}-s-${scorpio_VER}