Reema, Apologies for the slow response. This recent reply (see below) to another message on the mailing list from Ross deals with java tools in galaxy and might be of use to you. See also the tool integration tutorial here: https://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial Let me know if you need more information. -Dannon On May 7, 2011, at 10:10 AM, Ross wrote:

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.