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Orchestration with Docker Compose

Overview

Teaching: 20 min
Exercises: 20 min
Questions

  • How can I manage applications with multiple components

Objectives

  • Use Docker compose to deploy an OMERO installation

Docker compose (and other orchestration tools) make it easier to deploy applications consisting of multiple Docker containers.

Docker compose deploys an application described by a YAML file. There are multiple versions of the docker-compose format/schema. This example uses version 3.

Database

Start by creating a docker-compose.yml file for just PostgreSQL, including a private network and data volume:

services:

  database:
    image: "postgres:16"
    environment:
      - POSTGRES_USER=omero
      - POSTGRES_DB=omero
      - POSTGRES_PASSWORD=SeCrEtPaSsWoRd
    networks:
      - omero-network
    volumes:
      - "database-volume:/var/lib/postgresql/data"

networks:
  omero-network:

volumes:
  database-volume:

Compare this with the command in the previous lesson used to run the postgres container, the mapping between the Docker command-line parameters and the compose file should be clear.

Run docker compose in the directory containing your docker-compose.yml file:

docker compose -f docker-compose.yml up

Creating network "dockercompose_omero-network" with the default driver
Creating volume "dockercompose_database-volume" with default driver
Creating dockercompose_database_1 ...
Creating dockercompose_database_1 ... done
Attaching to dockercompose_database_1
...
database_1  | LOG:  database system is ready to accept connections

Next add omeroserver to the services and omero-volume to volumes:

services:

  database:
    image: "postgres:16"
    environment:
      - POSTGRES_USER=omero
      - POSTGRES_DB=omero
      - POSTGRES_PASSWORD=SeCrEtPaSsWoRd
    networks:
      - omero-network
    volumes:
      - "database-volume:/var/lib/postgresql/data"

  omeroserver:
    image: "openmicroscopy/omero-server:5.6.15"
    environment:
      - CONFIG_omero_db_host=database
      - CONFIG_omero_db_user=omero
      - CONFIG_omero_db_pass=SeCrEtPaSsWoRd
      - CONFIG_omero_db_name=omero
      - ROOTPASS=omero
    networks:
      - omero-network
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - "omero-volume:/OMERO"

networks:
  omero-network:

volumes:
  database-volume:
  omero-volume:

Run

docker compose -f docker-compose.yml up

and you should see both the database and OMERO.server running.

We now want to add omero-web and nginx to services. First we need to create a folder nginx in the directory where the docker-compose.yml file is. This folder will be “mounted”.

mkdir nginx
cd nginx

Then add to the nginx folder a file default.conf:


map $http_upgrade $connection_upgrade {
  default upgrade;
  '' close;
}

server {
  listen 80 default_server;
  server_name  $hostname;

  # Self-signed certificate for testing
  #listen 443 ssl;
  #ssl_certificate /etc/nginx/ssl/server.pem;
  #ssl_certificate_key /etc/nginx/ssl/server.key;

  resolver 127.0.0.11;

  location / {
    proxy_pass http://omeroweb:4080;
  }
}

Add a file nginx.conf:

user  nginx;
worker_processes  1;

error_log  /var/log/nginx/error.log debug;
pid        /var/run/nginx.pid;


events {
    worker_connections  1024;
}


http {
    include       /etc/nginx/mime.types;
    default_type  application/octet-stream;

    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    access_log  /var/log/nginx/access.log  main;

    sendfile        on;
    #tcp_nopush     on;

    keepalive_timeout  65;

    #gzip  on;

    include /etc/nginx/conf.d/*.conf;
}

We now add omero-web and nginx to services.

services:

  database:
    image: "postgres:16"
    environment:
      - POSTGRES_USER=omero
      - POSTGRES_DB=omero
      - POSTGRES_PASSWORD=SeCrEtPaSsWoRd
      - POSTGRES_HOST_AUTH_METHOD=trust
    networks:
      - omero-network
    ports:
      - "5432:5432"
    volumes:
      - ./pgdata:/var/lib/postgresql/data

  omeroserver:
    # This container uses the tag for the latest omero server release of OMERO 5
    image: "openmicroscopy/omero-server:5"
    environment:
      - CONFIG_omero_db_host=database
      - CONFIG_omero_db_name=omero
      - ROOTPASS=omero
    networks:
      - omero-network
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - omero-volume:/OMERO

  omeroweb:
    # This container uses the tag for the latest web release of OMERO 5
    image: "openmicroscopy/omero-web-standalone:5"
    environment:
      - OMEROHOST=omeroserver
      - CONFIG_omero_web_csrf__trusted__origins=["http://localhost:8080"]
    networks:
      - omero-network

  nginx:
    image: library/nginx:1.26
    networks:
      - omero-network
    ports:
      - "8080:80"
      - "8443:443"
    volumes:
      - ./nginx/log:/var/log/nginx
      - ./nginx/default.conf:/etc/nginx/conf.d/default.conf:ro${VOLOPTS-}
      - ./nginx/nginx.conf:/etc/nginx/nginx.conf:ro${VOLOPTS-}
      #- "./certs:/etc/nginx/ssl:ro${VOLOPTS-}"


networks:
  omero-network:
    # If it fails and your network has a non-standard MTU this may
    # need to be set if auto-detection fails
    driver_opts:
        com.docker.network.driver.mtu: 1450


volumes:
  omero-volume:

Run in detach mode i.e. you will be able to close the terminal and disconnect and the server will still be working.

docker compose -f docker-compose.yml up -d

and you should be able to log in to OMERO.web at http://localhost:8080.

To stop the container

Run

docker compose -f docker-compose.yml down

Key Points

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