/omero-server-docker

OMERO.server production docker image

Primary LanguageShell

OMERO.server Docker

A CentOS 7 based Docker image for OMERO.server.

Also see SUPPORT.md

Running OMERO with docker-compose

The omero-deployment-examples repository contains a number of different ways of deployment OMERO. Unless you are looking for something specific, we suggest starting with docker-example-omero.

Running the images (manual)

To run the Docker images start a postgres DB:

docker run -d --name postgres -e POSTGRES_PASSWORD=postgres postgres

Then run OMERO.server passing the database configuration parameters if they differ from the defaults. This example uses the default postgres system database for convenience, in practice you may want to create your own database.

docker run -d --name omero-server --link postgres:db \
    -e CONFIG_omero_db_user=postgres \
    -e CONFIG_omero_db_pass=postgres \
    -e CONFIG_omero_db_name=postgres \
    -e ROOTPASS=omero-root-password \
    -p 4063:4063 -p 4064:4064 \
    openmicroscopy/omero-server

Configuration variables

All OMERO configuration properties can be set be defining environment variables CONFIG_omero_property_name=. Since . is not allowed in a variable name . must be replaced by _, and _ by __, for example

-e CONFIG_omero_web_public_enabled=false

Configuration files

Additional configuration files for OMERO can be provided by mounting files into /opt/omero/server/config/. Files ending with .omero will be loaded with omero load.

For example:

docker run -d -v
    /config/extra.omero:/opt/omero/server/config/extra.omero:ro
    openmicroscopy/omero-server

Parameters required for initializing the server such as database configuration must be set using environment variables.

Default volumes

  • /opt/omero/server/OMERO.server/var: The OMERO.server var directory, including logs
  • /OMERO: The OMERO data directory

Exposed ports

  • 4063
  • 4064

Example with named volumes

docker volume create --name omero-db
docker volume create --name omero-data

docker run -d --name postgres -e POSTGRES_PASSWORD=postgres
    -v omero-db:/var/lib/postgresql/data postgres
docker run -d --name omero-server --link postgres:db
    <-e CONFIG_omero_db_ ...>
    -v omero-data:/OMERO
    -p 4063:4063 -p 4064:4064 openmicroscopy/omero-server

Running without links

As an alternative to running with --link the address of the database can be specified using the variable CONFIG_omero_db_host