Hey Christian,

I used <galaxy_dir>/scripts/db_shell.py and something like https://gist.github.com/dannon/e71b7aa9546fcecf6e9e to reset problematic BAM metadata.  Basically, it selects all the large metadata and completely strips out the new overly large optional attributes, leaving required attributes alone.  Once this is done, you can redetect metadata if you'd like (with the limits we'd talked about set) and it should all work fine.

Let me know if you need more info, hopefully this helps!


On Fri, Jul 24, 2015 at 11:23 AM Christian Schudoma (TSL) <Christian.Schudoma@sainsbury-laboratory.ac.uk> wrote:
Hi Nate, all

I would like to add my own version of the problem to this.

I, or rather my (inherited) Galaxy instance (which should be running 15.05+, how do I find out?), have/s similar symptoms as Richard's did. In my case it only occurs to a single user and we are not able to execute the "Saved Histories" command any more. Galaxy will fail with

Proxy Error

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /history/list.

Reason: Error reading from remote server

Due to some problem with the psql-client I cannot find the potential perpetrators (my user has lots of bam files in various histories) and since he cannot switch histories, we cannot even update the metadata for his datasets. Is there a possibility to do that via the API?

Any insight/help would be greatly appreciated!


On 08/07/15 21:04, Poole, Richard wrote:

I am having trouble right now with my own personal account on my production server. Grid refreshes are taking a huge amount of time (e.g. when viewing ‘saved histories’ or even generating the dataset list for a single history). My account is very full of data (1TB), could it be this?

There are no obvious messages in the logs though so I am a bit stumped as to why.I do not have the same trouble when impersonating other users with fairly full accounts. Perhaps a database issue (I do not know how to ‘cleanup’ the database or indeed Galaxy user accounts). Any thoughts?

Dr. Christian Schudoma
Bioinformatics Support Officer

Bioinformatics Group
The Sainsbury Laboratory
Norwich Research Park
Norwich NR4 7UH
United Kingdom
+44 (0) 1603 450 601

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