docker-compose.yml

version: '3'

services:
#Omero postgress database docker
  omero-db:
    container_name:
      omero-db
    image: postgres:10-alpine
    networks:
      ome_seadragon_env:
        aliases:
          - ome-pg-server
    environment:
      - POSTGRES_DB=${OMEROPGDB}
      - POSTGRES_USER=${OMEROPGUSER}
      - POSTGRES_PASSWORD=${OMEROPGPASSWORD}
    volumes:
      - ome-pg-data:/var/lib/postgresql/data
     # External postgres backup folder 
      - /mnt/db-backup:/mnt/db-backup
    restart:
      always
#Redis server docker
  redis-server:
    container_name:
      redis-server
    image: redis:5.0.5-alpine
    command: ["redis-server", "--appendonly", "yes"]
    networks:
      ome_seadragon_env:
        aliases:
          - redis-server
    volumes:
      - redis-data:/data
    restart:
      always
#Omero server docker
  omero-server:
    container_name:
      omero-server
    image: openmicroscopy/omero-server:5.6
    depends_on:
      - omero-db
    networks:
      ome_seadragon_env:
        aliases:
          - omero-server
    ports:
      - "4063:4063"
      - "4064:4064"
    environment:
      - ROOTPASS=${OMEROROOTPASSWORD}
      - CONFIG_omero_db_host=ome-pg-server
      - CONFIG_omero_db_user=${OMEROPGUSER}
      - CONFIG_omero_db_pass=${OMEROPGPASSWORD}
      - CONFIG_omero_db_name=${OMEROPGDB}
    volumes:
      # External omero data
      - /mnt/OMERO:/OMERO
      # External omero server configurations (read-only)
      - /mnt/omero_config/extra.omero:/opt/omero/server/config/extra.omero:ro
      - ome-server-var:/opt/omero/server/OMERO.server/var
    restart:
      always
#Ome seadragon web docker
  ome_seadragon-web:
    container_name:
      ome_seadragon-web
    image: crs4/ome_seadragon-web:0.6.16-ome5.5.1
    depends_on:
      - omero-server
      - redis-server
    entrypoint: ['/usr/local/bin/wait-for-it.sh', 'redis-server:6379', '--',
                 '/usr/local/bin/wait-for-it.sh', 'omero-server:4063', '--timeout=600', '--strict', '--',
                 '/usr/local/bin/wait-for-it.sh', 'omero-server:4064', '--timeout=600', '--strict', '--',
                 '/usr/local/bin/entrypoint.sh']
    networks:
      ome_seadragon_env:
        aliases:
          - ome_seadragon-web
    environment:
      - ROOTPASS=${OMEROROOTPASSWORD}
      - OMEROHOST=omero-server
      - REDISHOST=redis-server
      - IMAGES_REPOSITORY=/OMERO/
      - GW_USER_NAME=${GATEWAYPGUSER}
      - GW_USER_PASS=${GATEWAYPGPASSWORD}
    volumes:
      # External omero data (read-only)
      - /mnt/OMERO:/OMERO:ro
      # external omero server configurations (read-only
      - /mnt/omero_config/extra.omero:/opt/omero/server/config/extra.omero:ro
    restart:
      always
#Ome seadragon nginx webserver docker
  ome_seadragon-nginx:
    container_name:
      ome_seadragon-nginx
    image: crs4/ome_seadragon-nginx:0.6.16-ome5.5.1
    depends_on:
      - ome_seadragon-web
      - nginx-proxy
    entrypoint: ['/usr/local/bin/wait-for-it.sh', 'ome_seadragon-web:4080', '--timeout=600', '--strict', '--',
                 '/usr/local/bin/entrypoint.sh']
    networks:
      ome_seadragon_env:
        aliases:
          - ome_seadragon-nginx
          - ome-seadragon.local
    environment:
      - OMEROWEBHOST=ome_seadragon-web
      - VIRTUAL_HOST=${OMEROWEBSITE}
      - LETSENCRYPT_HOST=${OMEROWEBSITE}
    restart:
      always
#Ome seadragon gateway (with its own database) docker
  ome_seadragon_gw-db:
    container_name:
      ome_seadragon_gw-db
    image: postgres:10-alpine
    networks:
      ome_seadragon_env:
        aliases:
          - ome_seadragon_gw-db
    environment:
      - POSTGRES_DB=ome_seadragon_gw
      - POSTGRES_USER=ome_seadragon
      - POSTGRES_PASSWORD=${OMESDPGPASSWORD}
    volumes:
      - ome-seadragon-gw-pg-data:/var/lib/postgresql/data
     # External postgres backup folder 
      - /mnt/db-backup:/mnt/db-backup
    restart:
      always
#Ome seadragon gatweay django docker
  ome_seadragon_gw-web:
    container_name:
      ome_seadragon_gw-web
    image: crs4/ome_seadragon_gw-web:0.1.3
    depends_on:
      - ome_seadragon-nginx
      - redis-server
      - ome_seadragon_gw-db
    entrypoint: ['/usr/local/bin/wait-for-it.sh', 'redis-server:6379', '--',
                 '/usr/local/bin/wait-for-it.sh', 'ome_seadragon_gw-db:5432', '--',
                 '/usr/local/bin/wait-for-it.sh', 'ome_seadragon-nginx:80', '--timeout=600', '--strict','--',
                 '/usr/local/bin/entrypoint.sh']
    networks:
      ome_seadragon_env:
        aliases:
          - ome_seadragon_gw-web
    environment:
      - DJANGO_CONFIG_FILE=/opt/django/conf/config.yaml
    volumes:
      - ./ome_seadragon_gw_config/:/opt/django/conf/
    restart:
      always
#Ome seadragon gateway webserver docker
  ome_seadragon_gw-nginx:
    container_name:
      ome_seadragon_gw-nginx
    image: crs4/ome_seadragon_gw-nginx:0.1.3
    depends_on:
      - ome_seadragon_gw-web
      - nginx-proxy
    entrypoint: ['/usr/local/bin/wait-for-it.sh', 'ome_seadragon_gw-web:8080', '--timeout=600', '--strict', '--',
                 '/usr/local/bin/entrypoint.sh']
    networks:
      ome_seadragon_env:
        aliases:
          - ome_seadragon_gw-nginx
          - ome-seadragon-gw.local
    environment:
      - DJANGO_SERVER=ome_seadragon_gw-web
      - VIRTUAL_HOST=${OMESDWEBSITE}
      - LETSENCRYPT_HOST=${OMESDWEBSITE}
    restart:
      always
#Nginx proxy server docker  
  nginx-proxy:
    container_name: 
      nginx-proxy
    image: 
      jwilder/nginx-proxy
    networks:
      ome_seadragon_env:
        aliases:
          - nginx-proxy
    ports:
      - "80:80"
      - "443:443"
    volumes:
     # External nginx config backup folder 
      - /mnt/nginx-backup:/mnt/nginx-backup
      - nginx-proxy-conf:/etc/nginx/conf.d
      - nginx-proxy-certs:/etc/nginx/certs:ro
      - nginx-vhostd:/etc/nginx/vhost.d
      - nginx-engine-html:/usr/share/nginx/html
      - nginx-dhparam:/etc/nginx/dhparam
      - /var/run/docker.sock:/tmp/docker.sock:ro
    restart:
      always
#Proxy letsencrypt addition
  nginx-proxy-letsencrypt:
    container_name: 
      letsencrypt-companion
    image: 
      jrcs/letsencrypt-nginx-proxy-companion
    depends_on:
      - nginx-proxy
    networks:
      ome_seadragon_env:
        aliases:
          - nginx-proxy-letsencrypt
    volumes:
      - nginx-proxy-conf:/etc/nginx/conf.d
      - nginx-proxy-certs:/etc/nginx/certs:rw
      - nginx-vhostd:/etc/nginx/vhost.d
      - nginx-engine-html:/usr/share/nginx/html
      - nginx-dhparam:/etc/nginx/dhparam
      - /var/run/docker.sock:/var/run/docker.sock:ro
    environment:
      - DEFAULT_EMAIL=${EMAILSSL}
      - NGINX_PROXY_CONTAINER=nginx-proxy
    restart: 
      always
#End of containers session
volumes:
  ome-pg-data: null
  ome-seadragon-gw-pg-data: null
  ome-server-var: null
  # ome-data-dir: null
  redis-data: null
  nginx-proxy-conf: null
  nginx-proxy-certs: null
  nginx-vhostd: null
  nginx-engine-html: null
  nginx-dhparam: null
networks:
  ome_seadragon_env: null