OK, this pointed me to the right direction.
The universe_wsgi.ini file has a key that reads:
database_connection =
sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
This entry was commented out in my version of the file (ie, had a # in
front of it). While Galaxy itself uses this
Klaus,
I'm getting this too. I tried yesterday fro the first time to clean up my
local Galaxy data. (I was trying to purge all data and histories, ie. reset
the database to as-new). This is in a Galaxy download and install done on
12 March 2012. I'd give you the hg -heads/summary and some other
