> Why are Custom Builds only enabled if you're *not* using remote_user ?
> Is this because they're related to user preferences (as per the code in
> lib/galaxy/webapps/galaxy/controllers/user.py)?

This may be an artifact of a time when user preferences were immutable. Do 
Custom Builds and Preferences work on your set up using remote users?

> And then a followup, if I have to add a build using either a FASTA file
> or a lenfile and editing the Galaxy install on the server, where do I
> need to make changes?

Unfortunately, It'll go in different places depending on your use. What are you 
looking to do with the build? 

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