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?


Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to