Sumedha Ganjoo wrote:

Hi,

I am using a tool that interacts with Web services via Galaxy. Run on its own in the Galaxy GUI, it works fine. But when we run it in a workflow, with other tools it sometimes runs correctly , sometimes gives the following error:

OperationalError: (OperationalError) database is locked u'UPDATE job SET update_time=?, command_line=? WHERE job.id = ?' ['2010-07-12 14:10:18.398960', 'python ${installationDirectory}/tools/${............ .....................................................

I was wondering if Galaxy has some timeouts implemented in their workflows because of which if the first step takes a while the second step of the workflow is executed simultaneously? Or any other explanation for such behavior.

I would really appreciate a reply as soon as possible.

Hi Sumedha,

I'm guessing you're using the SQLite database. This problem should go away if you switch to Postgres. Please see the Production Server page in the wiki (which, incidentally, I just updated) for more information:

http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer

--nate

Thanks.

Regards, Sumedha