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.