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.