OMERO.web Docker

A RockyLinux 9 based Docker image for OMERO.web.

Also see SUPPORT.md

Running OMERO with docker-compose

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

Standalone image: omero-web-standalone

The quickest way to obtain a running OMERO.web server is to use the standalone image which uses the WhiteNoise package to avoid the need for Nginx. This image also includes these OMERO.web plugins with a default configuration:

• figure
• iviewer
• mapr
• parade
• autotag
• tagsearch

The following plugins are installed but disabled:

• fpbioimage

To enable them or to change the configuration of a default plugin see the relevant plugin documentation.

To run the Docker image you can set a single OMERO.server to connect to by defining OMEROHOST:

docker run -d --name omero-web-standalone \
    -e OMEROHOST=omero.example.org \
    -p 4080:4080 \
    openmicroscopy/omero-web-standalone

Alternatively, all configuration options can be set using environment variables, for example, add the following arguments to the command above:

    -e CONFIG_omero_web_server__list='[["omero.example.org", 4064, "omero"]]' \
    -e CONFIG_omero_web_debug=true \

The $OMERODIR is /opt/omero/web/OMERO.web/ so you can have the logs written to your host by adding:

    -v /path/to/host/dir:/opt/omero/web/OMERO.web/var/logs \

Minimal OMERO.web image: omero-web

omero-web is a minimal OMERO.web image which requires additional configuration for serving Django static files. For example, you can use https://github.com/dpwrussell/omero-nginx-docker

Configuration

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 __.

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

See https://github.com/openmicroscopy/omero-server-docker for more details on configuration.

Default volumes

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

Exposed ports

• 4080

Development

You can use this repository to build a custom image for testing development builds of OMERO.web. For example, to install OMERO.web from the OMERO-build CI job:

make VERSION=test REPO=test BUILDARGS="\
    --build-arg OMEGO_ADDITIONAL_ARGS=--ci=https://web-proxy.openmicroscopy.org/west-ci/ \
    --build-arg=OMERO_VERSION=OMERO-build" docker-build

docker run -d --name test-web \
    -e CONFIG_omero_web_server__list='[["eel.openmicroscopy.org", 4064, "eel"]]' \
    -e CONFIG_omero_web_debug=true \
    -p 4080:4080 \
    test/omero-web-standalone:latest