Hi Frederick, I'm not an expert but maybe you could consider to write a python wrapper to call your Java application.

--- Marco

On 7 May 2011 08:08, Frederick van Staden cmptrwizard@gmail.com wrote:

Hello!

Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue.

Anyone that could guide me in the right direction?

Regards Frederick

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There are a growing number of tools based on java packages - perhaps the example in tools/sr_mapping/srma_wrapper.xml could be a useful 'simple' starting point?

For more complex scenarios, there are a number of new Picard based java tools (only exposed on test at present) in the galaxy-central source tree under tools/picard that do even more complex integration of multiple outputs into html output files.

The relevant jars are all placed in tool-data/shared/jars and that path is passed in the xml command template as something like:

--jar="${GALAXY_DATA_INDEX_DIR}/shared/jars/foo.jar"

Of course YMMV depending on your specific needs but this approach certainly can be made to work for java packages like Picard and FastQC.

On Sat, May 7, 2011 at 2:08 AM, Frederick van Staden cmptrwizard@gmail.comwrote:

Hello!

Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue.

Anyone that could guide me in the right direction?

Regards Frederick

---

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/