Hello all,

I recently tried moving from a tarball install of Galaxy to a Mercurial
managed one, and in the process something went wrong with the database
upgrade. I had intended to install the Mercurial-based Galaxy separately
(though on the same machine) and then move it to production once it was
working but it installed in-place over the current database while it was
still completely active/up and running. That broke  my existing Galaxy
install and I had to move to the new install immediately. I recall having
to run the Mercurial install's run.sh script multiple times though because
the upgrade sequence (looked like 87->88, 88->89, etc. as it progressed)
did not complete all the way the first time. I also ran it as root when I
probably should have done it as our galaxy user. Long story short now I
cannot log in to Galaxy even though Galaxy recognizes correct credentials
from the database. My debugging so far has not yielded any results.

At this point after a week of unsuccessful attempts to repair the existing
install I just want to create a fresh database and migrate over our users'
history and dataset (and possibly login credentials) information stored in
the database to the new one, if at all possible. Could someone give me any
guidance as to how to do that, and which table files (MYI, MYD, etc.) that
I should copy over into the new mysql database to make that happen?

P.S. I do have to thank Dannon Baker for helping me so far through private
email correspondence to try to figure out what went wrong with the current
install. However I'm not having any breakthroughs and our local Galaxy
mirror has been down for over a week now and I just want to start fresh and
migrate over critical data if possible.

Thanks for your help,
Josh Nielsen
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