On Wed, Feb 23, 2011 at 10:58:18PM -0500, Nate Coraor wrote:
It looks like your datatypes_conf.xml is out of date. Have a look at the differences from datatypes_conf.xml.sample.
Ooof, I've been merging in regularly, but in a strictly additive fashion. I think my disconnect came in not understanding why those warnings would abort for a remote runner but not for the local runner, which I now realize is because the local runner isn't re-initializing the entire galaxy stack and re-parsing the config file, so on local I see those warnings at startup time where they're not blocking a job.
Is it possible it's just the output on STDERR causing the job to fail, and if so how do I shut that up when I'm running through qsub (so redirect to /dev/null isn't quite right)?
Yes, anything output to STDERR will be considered a failure. There is a ticket in Bitbucket for this (actually, you commented on it 8 months ago ;)
https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-...
Heh, not just commented but had the call to do a 'take' on it, though the good folks who have done more with it since have taken it back. Thanks! -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu