I was having an issue with the Data Manager to fetch reference genomes and after checking to see if there was a newer version of galaxy, I decided to update and see if that fixed my problem.

I ran "hg pull" and then "hg update latest_2014.06.02". I tried to rerun galaxy but was instructed to run manage_db.sh so I did (sh manage_db.sh upgrade).

When I ran galaxy after all this, it started but when opened in a web browser, the navagation pane at the top is missing (i.e. Analyze Data, Workflows, User, etc). There is a blue bar but nothing is on it.

How do I get the missing navigation pane back? I can't do a lot of things without it (i.e. check help or change user settings). I can still get to the administrator section but only by appending "/admin" to the url. I need to know how to fix the new version or how to succesfully revert to a previous version without anything else breaking.