Well I know there is a way to make a custom tech tree but I can't find where buildings are dependent on others. For instance the Gateway needs the Nexus, but I want the Nexus to require the Gateway.

The tech tree is done through requirements. So in the build ability for the probe there is an Info property which has all the buildings a probe can make. For each building (double click on a building) you can set a requirement for it.

And requirements can be edited, of course.