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'
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:
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
> 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?
> 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:
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;
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: