Hi,

during tool execution the env variables will be set and all requirements will be tried to resolved. Can you see at the galaxy log file during the tool execution? You will see something like:


Building dependency shell command for dependency ...

Does that seems to be correct?
Bjoern

Am 17.03.2014 16:54, schrieb Alexander Kurze:
Hi Bjoern,

thanks for your quick answer.

My path to my picard is /home/galaxy/shed_tools/
toolshed.g2.bx.psu.edu/repos/devteam/picard/bf1c3f9f8282/picardunfortunately
I cannot find a env.sh in there.
The env.sh is in the dependency folder
/home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f
The env.sh points to the right folder
JAVA_JAR_PATH=/home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f/jars;
export JAVA_JAR_PATH

Any suggestions?

Alex


On Mon, Mar 17, 2014 at 3:31 PM, Björn Grüning <bjoern.gruen...@gmail.com>wrote:

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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