Gavin:
I'd recommend you read the script I linked earlier it sets up a VistA instance on GT.M in a sane way ensures that permissions are correct, creates an example programmer tied user, an example VistA tied user and all of the scripts required to make the tied users work.
There are other scripts which take care of other things in the repository which is designed to get a development environment setup quickly and sanely. If you have questions about the scripts please ask as there are created for the benefit of the community and being the developer I'm always interested in feedback. These scripts already contain lots of community input and wholesome practices for how to setup VistA from a Linux system administration point of view.
Thanks!