Running ODK with Podman¶
Some employers, in particular outside academia, may discourage the use of Docker via Docker Desktop for licensing reasons. Podman is an open source container, pod, and container image management engine. While there are some fundamental differences between Podman and Docker, a basic user can treat them as largely equivalent, for example by creating an alias from Podman's native podman command to Docker's docker.
Aliases work well for running docker commands directly but it create some issues around automatic processes in ODK since a locally set alias is not visible from ODK's run.sh script. As a result, a command like
may give you the error message
./run.sh: line 68: docker: command not found
Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/.
To fix this, instead create a symlink between docker and the Podman executable. To do this, run
to find where podman is installed, then navigate to the Podman executable
Now create the symlink using (requires admin privileges)
After this, running ls -la in the same directory should include a line like
and which docker should return
Finally, ensure that the symlink is somewhere on your path (if it isn't already!) by running
Restart your shell and you should find that your ODK run.sh script works again as expected.
Warning!¶
The commands above were tested in zsh shell on a Mac. They should also work in an bash shell, on Mac or Linux. They may not work on Windows.
You could also edit the ODK run.sh script to use podman instead of docker, which would work with the previously mentioned alias solution but this is NOT ADVISABLE as the change would be overwritten every time the repo is updated. Plus, if your run.sh is committed into your Git repo, the change would affect all your fellow ontology editors.