In section Chapter 1 - Setup, instead of instructing users to use apt to install docker, a better approach would be to direct them to official documentation for installing docker. This leaves the decision up to the user for how they wish to install it and they are likely guaranteed to install the latest stable version instead of a version from the apt repo that may be old and performs differently than what is expected by your iRODS specific documentation.

An alternative to this is that you could document what version of docker the documentation is using. That would give users a minimum version for what they need to reproduce what is presented.

Ultimately, your documentation is not responsible for telling users how to meet all prerequisites. In my opinion, there is adequate documentation for setting up external tools and therefore we should leverage that documentation (when we can) and maybe provide direct links to the steps within that documentation to expedite and simplify setup.