2019 Edit: If you want to use a Dockerfile and custom image take a look a here.
Just over a month ago I setup the Wikibase registry project on Wikimedia Cloud VPS using the docker-compose example provided by Wikibase docker images. The Wikibase registry is the first Wikibase install that I control that uses the Wikibase docker images, so I’ll be using it as an example showing how the docker images can be manipulated to configure MediaWiki, Wikibase, and load custom extensions and skins.
The example docker-compose file at the time of writing this post can be found at https://github.com/wmde/wikibase-docker/blob/5919016eac16c5f0aefc448240fdf6a09bb56bec/docker-compose.yml
Since the last blog post new wikibase image tags have been created (the ‘bundle’ tags) that include some extensions you might want to enable, as well a quickstatements image for the quickstatements service used on Wikidata written by Magnus Manske.