openmicroscopy/omero-deploy repository overview

⁠omero-deploy

An all-in-one image (including postgres and nginx) for testing OMERO.server. This is not recommended for production use.

To download, install and run the default server in the background:

docker run -d -p 8080:80 -p 4063:4063 -p 4064:4064 openmicroscopy/omero-deploy

This will immediately return an ID that you can use to follow the logs:

docker logs -f <container-id>

or remove the -d flag to run in the foreground.

omego⁠ is used to download and install the server when the image is started (defaults to the latest release). Command arguments are appended to the omego command line. For example, an alternative release, a CI build, or the URL to an alternative OMERO.server zip, can be passed:

docker run -d openmicroscopy/omero-deploy --release 5.1.4
docker run -d openmicroscopy/omero-deploy --branch OMERO-DEV-merge-build
docker run -d openmicroscopy/omero-deploy https://download.example.org/OMERO.server-X.zip

Pass "" to disable the automatic server installation.

docker run -d openmicroscopy/omero-deploy ""

This will start all the required services so the server can be installed manually:

CID=$(docker run -d openmicroscopy/omero-deploy "")
docker exec $CID /omero-setup --release latest

⁠Passwords

Define the following environment variables to set the initial passwords:

• OMERO_PASSWORD: OMERO.server root password (default omero, ignored if an existing OMERO database is being used)
• SYSTEM_PASSWORD: The omero user system password (default unset, must be set to allow ssh login)

Example:

docker run -d -e SYSTEM_PASSWORD=abc -e OMERO_PASSWORD=def openmicroscopy/omero-deploy

⁠Data volumes

/data is defined as a volume. The following directories may be used or created:

• /data/OMERO: OMERO data directory
• /data/postgresql: PostgreSQL data directory
• /data/supervisor: Supervisord logs
• /data/omero.preload: Optional scripts to be passed to bin/omero load ... before starting the server

⁠Notes

This image is designed for testing and debugging OMERO, and includes:

• ssh
• password-less sudo for the omero user