[Docker] How to run own commands?

Too late but it might help fellows.

This is dangerous as remove-unkown is designed to be run with the server down.

stop your docker container for the server:
docker stop urbackup

start a docker container running urbackupsrv with the argument you want by using docker CMD:

version: '2'

services:
  urbackup:
    image: uroni/urbackup-server:latest
    container_name: urbackup_remove-unknown
    command: remove-unknown
    environment:
        - PUID=1002 # Enter the UID of the user who should own the files here
        - PGID=100  # Enter the GID of the user who should own the files here
        - TZ=Europe/Paris # Enter your timezone
    volumes:
      - /srv/dev-disk-by-label-secure/appdata/docker/urbackup/etc_default_urbackupsrv:/etc/default/urbackupsrv
      - /srv/dev-disk-by-label-secure/appdata/docker/urbackup/var_urbackup:/var/urbackup
      - /srv/dev-disk-by-label-secure/appdata/docker/urbackup/var_log:/var/log
      - /srv/dev-disk-by-label-secure/backup/urbackup:/backups
    cap_add:
      - SYS_ADMIN # Activate the following two lines for BTRFS support

I added that snippet as a portainer stack but you should be able to run it with docker compose.

Once this remove-unknown container is created, you can start it with:
docker start urbackup_remove-unknown

I did not find a way to stop the server container when I ran the remove-unknown one. So you have to think about stopping the daemon container before running the remove-unknown one.