Hi Alex,

can you check if all dependencies are installed. Afaik Galaxy sets an env variable to point to the actual jar file. That env variable is missing and the constructed path to your picard executable is looking like $SOME_NOT_SET_ENV_VAR/ReorderSam.jar.


Hope that helps,
Bjoern

Am 17.03.2014 15:48, schrieb Alexander Kurze:
Hi there,
we are running a local instant of galaxy and when running Picard tools
Reorder Sam files I get following error message:

"An error occurred with this dataset: *## exit code=1; stdout= Error:
Unable to access jarfile /ReorderSam.jar*"

Now, I thought that when installing picard-tools via the toolshed the
dependency should be added automatically. I am really not sure why it looks
for ReorderSam.jar in the top directory /. Any clues?

Best wishes,

Alex




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