Hi JJ,

On Feb 13, 2014, at 11:00 AM, Jim Johnson <johns...@umn.edu> wrote:

> I now have 2 versions of snpeff installed from the toolshed on my galaxy 
> server.   
> Each snpeff version includes an identical datatypes_conf.xml  
> The galaxy server is setting metadata externally.  
> When any job runs, (in may case I was running a picard tool), the following 
> message is written to the job stderr:
> WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with 
> extension 'snpeffdb', using datatype from /galaxy/database/tmp/tmpdKGVnQ.
> Without stdio tags or otherwise catching the stderr, the job state is set to 
> error.  

I believe I'm responsible for the above warning message, but I'm not sure I 
like the resulting behavior - I wasn't aware that the job runner now captures 
warning messages like this and sets the job state to error.  At the time I 
enhance the Galaxy datatypes components to work with the Tool Shed, this was 
not the behavior.

> I'm now assuming that best practice would be to put the datatypes in a 
> separate toolshed repository that would be a dependency for the tools 
> repository.
> Thus the datatypes would not loaded multiple times and avoid overrride 
> conflicts.  

Yes, the above plan would be a "best practice".

> In the meantime, I have just commented out the warning message.   
> Any other advice on this issue?

I'm wondering if we should just eliminate the warning message altogether sicne 
it now results in jobe errors.  Do others agree?

> Thanks,
> JJ
> -- 
> James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

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