Hi Hans,

OK, thanks: diving into the job table. Your question: "why you consider the job as being finished, and Galaxy thinks the job is still running" is the core issue that I need to find out. None of those jobs have entries in the ps list.

Currently, I think that those jobs are still listed because they were not nicely shut down by Galaxy, but because of a crash (e.g. of the virtual machine). Upon restarting Galaxy, Galaxy seems not to check whether those jobs are currently running, but seems to depend entirely on the job table to fill the 'unfinished jobs' table.

Cheers, Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

On 03/07/2013 11:21 AM, Hans-Rudolf Hotz wrote:

Hi Joachim

...

I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished.

Any hint on how to clean up the database? Which table? Perhaps I can make a Trello card: 'Provide a button to remove the jobs from the unfinished jobs page' ?

Well, you can modify the entries in the 'job' table.....As always, be very careful when you directly access the MySQL or PostgreSQL database.

In your case I would set the state to 'error', eg:

update job set state='error' where id=123456789;

Once again be careful. I would examine each job individually. And try to figure out, why you consider the job as being finished, and Galaxy thinks the job is still running

Regards, Hans-Rudolf

...

Thanks for taking me further, Joachim