Some analysis scripts appear not to run with newer data formats or require special configurations

[markwhiting]

In the spirit of open science, we should move toward storing everything in a way that anyone can run it with what is in the repo.

This will be considered done when

• we can run everything on a new machine without issues (with no assumptions about paths and with all installation requirements included in the scripts).
• data are stored locally in a suitably anonymous way so that remote calls aren't needed to process or review the data

[markwhiting]

@xehu can you double check this works and make any adjustments to remove any local calls in your scripts. (if you've already done that, great and lets mark it done)