Commands you use with `run` start in new containers with the same configuration as defined by the service' configuration. This means the container has the same volumes, links, as defined in the configuration file. There two differences though.
First, the command passed by `run` overrides the command defined in the service configuration. For example, if the `web` service configuration is started with `bash`, then `docker-compose run web python app.py` overrides it with `python app.py`.
The second difference is the `docker-compose run` command does not create any of the ports specified in the service configuration. This prevents the port collisions with already open ports. If you *do want* the service's ports created and mapped to the host, specify the `--service-ports` flag:
$ docker-compose run --service-ports web python manage.py shell
If you start a service configured with links, the `run` command first checks to see if the linked service is running and starts the service if it is stopped. Once all the linked services are running, the `run` executes the command you passed it. So, for example, you could run:
$ docker-compose run db psql -h db -U docker
This would open up an interactive PostgreSQL shell for the linked `db` container.
If you do not want the `run` command to start linked containers, specify the `--no-deps` flag:
$ docker-compose run --no-deps web python manage.py shell