I've gone ahead and made the change in the datatypes registry to use log.debu
instead of log.warning, so hopefully this issue is resolved. The changeset in
central is 12497:0b0018fa5d20, which has also be grafted to stable.
Greg Von Kuster
On Feb 13, 2014, at 11:51 AM, Jim Johnson johns...@umn.edu wrote:
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 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.
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?
Thanks,
JJ
--
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.
JJ
--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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