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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:

version: "3"

services:

  database:
    image: "postgres:9.6"
    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 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:

version: "3"

services:

  database:
    image: "postgres:9.6"
    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:5.4.0"
    environment:
      - CONFIG_omero_db_host=database
      - CONFIG_omero_db_user=omero
      - CONFIG_omero_db_pass=SeCrEtPaSsWoRd
      - CONFIG_omero_db_name=omero
      - ROOTPASS=omero-root-password
    networks:
      - omero-network
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - "omero-volume:/OMERO"

networks:
  omero-network:

volumes:
  database-volume:
  omero-volume:

Run

docker-compose up

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

Finally add omero-web to services:

version: "3"

services:

  database:
    image: "postgres:9.6"
    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:5.4.0"
    environment:
      - CONFIG_omero_db_host=database
      - CONFIG_omero_db_user=omero
      - CONFIG_omero_db_pass=SeCrEtPaSsWoRd
      - CONFIG_omero_db_name=omero
      - ROOTPASS=omero-root-password
    networks:
      - omero-network
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - "omero-volume:/OMERO"

  omeroweb:
    image: "openmicroscopy/omero-web-standalone:master"
    environment:
      - OMEROHOST=omeroserver
    networks:
      - omero-network
    ports:
      - "4080:4080"

networks:
  omero-network:

volumes:
  database-volume:
  omero-volume:

Run

docker-compose up

and you should be able to log in to OMERO.web at http://localhost:4080.

If you are feeling lazy you can download the complete docker-compose.yml file

Modifying the OMERO configuration

Modify docker-compose.yml to include some non-default configuration, for example enable a public user in OMERO.web

Solution

Add the following to the omeroweb environment:

- CONFIG_omero_web_public_enabled=True
- CONFIG_omero_web_public_user=root
- CONFIG_omero_web_public_password=omero-root-password
- CONFIG_omero_web_public_url__filter=^/

This is intended to be a quick example, you should obviously avoid using root as your public user in production.

Key Points

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