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?

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?)


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