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 -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341
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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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.gruening@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
___________________________________________________________ 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: http://lists.bx.psu.edu/
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-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341
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.gruening@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
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Alexander Kurze -
Björn Grüning