a few things we came across:
a, local install
R - not the correct download url, rpy - will this be fixed?
the script seems to use sudo and galaxy interchangeably, which creates an issue with permissions writing to folders.
Is there a way to install as galaxy user only?
If we do need the switching between sudo and galaxy - is there a set of directory permissions you suggest for the original galaxy-dist install and the galaxyToools folder?
b, as a second category of questions: are there any tools that do not work on the standard cloud install? (skipped over entirely or installed but do not work?)