Hi,

   I am trying to integrate a tool that is written in java into galaxy. The following is what I've done.

1) Created a directory inside /tools directory and put my xml and runnable jar file in it.

2) Linked the xml file in 'tool_conf.xml'.

tool_conf.xml

        <section name="sample tool" id="sample_tool">

<tool file="Sample/sample.xml"/>

</section>

sample.xml

        <tool id="sample" name="Compute correlation">
               <command>java -jar sample.jar</command>
        </tool>

sample.java (exported into a runnable jar file from eclipse)

         package Sample;

         public class Sample 

         {

         public static void main(String[] args)

         {

          System.out.println("Hello world this is important");

         }

         }

When I run the above, (i.e when I click on execute in the middle pane), nothing gets added to my current history. Since there is no visual output of any sort, I am not able to figure out where the problem lies. 

Any help or pointer is appreciated!

Thanks y'all!

VJ.

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