One way of copying a file would be to do it from the container. If you have a running container, use
docker cp to transfer the file to your host, in this case the EB instnace.
docker ps to get the container ID. If you don't see any output, launch a container based on the image you are interested in. Say, if your image name is 'aws-beanstalk/current-app' -
docker run -ti --rm aws-beanstalk/current-app /bin/bash
Then from the docker host, for instance to transfer a file under /code/run.py on the container to /tmp on the host:
docker cp containerID:/code/run.py /tmp
The containerID is the one you see after running
You can also use
docker exec -ti containerID /bin/bash to interactively work on an already running container.