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 It looks like your datatypes_conf.xml is out of date.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-decide-whether-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
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