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'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.

In the meantime, I have just commented out the warning message.

Any other advice on this issue?

Thanks,

JJ

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