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.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;