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
<cmptrwiz...@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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-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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