On 2/13/14, 10:22 AM, Greg Von Kuster wrote:
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 
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 
Yes, the above plan would be a "best practice".
Though I could still have some issues on my test galaxy instance,
since I often have tools from both the toolshed and testtoolshed simultaneously.

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?


James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
Or we could move it to log.debug level, which wouldn't usually be set on a 
production server.


James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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