How to run a command once in Docker compose

So I'm working on a docker compose file to deploy my Go web server. My server uses mongo, so I added a data volume container and the mongo service in docker compose.
Then I wrote a Dockerfile in order to build my Go project, and finally run it.

However, there is another step that must be done. Once my project has been compiled, I have to run the following command:
./my-project -setup

This will add some necessary information to the database, and the information only needs to be added once.
I can't however add this step on the Dockerfile (in the build process) because mongo must already be started.

So, how can I achieve this? Even if I restart the server and then run again docker-compose up I don't want this command to be executed again.

I think I'm missing some Docker understanding, because I don't actually understand everything about data volume containers (are they just stopped containers that mount a volume?).
Also, if I restart the server, and then run docker-compose up, which commands will be run? Will it just start the same container that was now stopped with the given CMD?

In any case, here is my docker-compose.yml:

version: '2'
services:
  mongodata:
    image: mongo:latest
    volumes:
      - /data/db
    command: --break-mongo
  mongo:
    image: mongo:latest
    volumes_from:
      - mongodata
    ports:
      - "28001:27017"
    command: --smallfiles --rest --auth
  my_project:
    build: .
    ports:
      - "6060:8080"
    depends_on:
      - mongo
      - mongodata
    links:
      - mongo

And here is my Dockerfile to build my project image:

FROM golang

ADD . /go/src/my_project
RUN cd /go/src/my_project && go get
RUN go install my_project
RUN my_project -setup
ENTRYPOINT /go/bin/my_project

EXPOSE 8080

I suggest to add an entrypoint-script to your container; in this entrypoint-script, you can check if the database has been initialized, and if it isn't, perform the required steps.

As you noticed in your question, the order in which services / containers are started should not be taken for granted, so it's possible your application container is started before the database container, so the script should take that into account.

As an example, have a look at the official WordPress image, which performs a one-time initialization of the database in it's entrypoint-script. The script attempts to connect to the database (and retries if the database cannot be contacted (yet)), and checks if initialization is needed; https://github.com/docker-library/wordpress/blob/df190dc9c5752fd09317d836bd2bdcd09ee379a5/apache/docker-entrypoint.sh#L146-L171

NOTE

I notice you created a "data-only container" to attach your volume to. Since docker 1.9, docker has volume management, including naming volumes. Because of this, you no longer need to use "data-only" containers.

You can remove the data-only container from your compose file, and change your mongo service to look something like this;

  mongo:
    image: mongo:latest
    volumes:
      - mongodata:/data/db
    ports:
      - "28001:27017"
    command: --smallfiles --rest --auth

This should create a new volume, named mongodata if it doesn't exist, or re-use the existing volume with that name. You can list all volumes using docker volume ls and remove a volume with docker volume rm <some-volume> if you no longer need it

You could try to use ONBUILD instruction:

The ONBUILD instruction adds to the image a trigger instruction to be executed at a later time, when the image is used as the base for another build. The trigger will be executed in the context of the downstream build, as if it had been inserted immediately after the FROM instruction in the downstream Dockerfile.

Any build instruction can be registered as a trigger.

This is useful if you are building an image which will be used as a base to build other images, for example an application build environment or a daemon which may be customized with user-specific configuration.

For example, if your image is a reusable Python application builder, it will require application source code to be added in a particular directory, and it might require a build script to be called after that. You can’t just call ADD and RUN now, because you don’t yet have access to the application source code, and it will be different for each application build. You could simply provide application developers with a boilerplate Dockerfile to copy-paste into their application, but that is inefficient, error-prone and difficult to update because it mixes with application-specific code.

The solution is to use ONBUILD to register advance instructions to run later, during the next build stage.

Here’s how it works:

1. When it encounters an ONBUILD instruction, the builder adds a trigger to the metadata of the image being built. The instruction does not otherwise affect the current build.
2. At the end of the build, a list of all triggers is stored in the image manifest, under the key OnBuild. They can be inspected with the docker inspect command.
3. Later the image may be used as a base for a new build, using the FROM instruction. As part of processing the FROM instruction, the downstream builder looks for ONBUILD triggers, and executes them in the same order they were registered. If any of the triggers fail, the FROM instruction is aborted which in turn causes the build to fail. If all triggers succeed, the FROM instruction completes and the build continues as usual.
4. Triggers are cleared from the final image after being executed. In other words they are not inherited by “grand-children” builds.

In docker-compose you can define:

restart: no

To run the container only once, which is useful for example for db-migration containers.

Your application need some initial state for working. It means that you should:

1. Check if required state already exists
2. Depends on first step result init state or not

You can write program for checking current database state (here I will use bash script but it can be every other language program):

RUN if $(./check.sh); then my_project -setup; fi

In my case if script will return 0 (success exit status) then setup command will be called.