On Thu, Feb 13, 2014 at 4:22 PM, Greg Von Kuster <g...@bx.psu.edu> 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 
>> 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.

Anything on stderr from a tool has always been treated as an error
(which I think was a bad design choice with hindsight). Had something
changed with regards to something like the external metadata tasks
being run as part of the job?

>> 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?

Probably...

Peter
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