Using heudiconv in a Container¶
If heudiconv is installed via a Docker container, you can run the commands in the following format:
docker run nipy/heudiconv:latest [heudiconv options]
So a user running via container would check the version with this command:
docker run nipy/heudiconv:latest --version
Which is equivalent to the locally installed command:
heudiconv --version
Bind mount¶
Typically, users of heudiconv will be operating on data that is on their local machine. We can give heudiconv access to that data via a bind mount, which is the -v syntax.
Once common pattern is to share the working directory with -v $PWD:$PWD, so heudiconv will behave as though it is installed on your system. However, you should be aware of how permissions work depending on your container toolset.
Docker Permissions¶
When you run a container with docker without specifying a user, it will be run as root.
This isn’t ideal if you are operating on data owned by your local user, so for Docker it is recommended to specify that the container will run as your user.:
docker run --user=$(id -u):$(id -g) -e "UID=$(id -u)" -e "GID=$(id -g)" --rm -t -v $PWD:$PWD nipy/heudiconv:latest --version
Podman Permissions¶
When running Podman without specifying a user, the container is run as root inside the container, but your user outside of the container. This default behavior usually works for heudiconv users:
docker run -v $PWD:PWD nipy/heudiconv:latest --version
Other Common Options¶
We typically recommend users make use of the following flags to Docker and Podman
-itInteractive terminal--rmRemove the changes to the container when it completes