Hi,<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br></div><div>   I am trying to integrate a tool that is written in java into galaxy. The following is what I&#39;ve done.</div>
<div><br></div><div>1) Created a directory inside /tools directory and put my xml and runnable jar file in it.</div>
<div>2) Linked the xml file in &#39;tool_conf.xml&#39;.<br></div><div><br></div><div><u>tool_conf.xml</u></div><div><br></div><div><div>        &lt;section name=&quot;sample tool&quot; id=&quot;sample_tool&quot;&gt;</div>

<div><span style="white-space:pre-wrap">		</span>&lt;tool file=&quot;Sample/sample.xml&quot;/&gt;</div><div><span style="white-space:pre-wrap">	</span>&lt;/section&gt;</div></div><div><br>
</div><div><u>sample.xml</u></div><div><br></div>        &lt;tool id=&quot;sample&quot; name=&quot;Compute correlation&quot;&gt;<br>               &lt;command&gt;java -jar sample.jar&lt;/command&gt;<br>        &lt;/tool&gt;<div>

<br></div><div><u>sample.java</u> (exported into a runnable jar file from eclipse)</div><div><br></div><div><div>         package Sample;</div><div>         public class Sample </div><div>         {</div><div><span style="white-space:pre-wrap">	</span>         public static void main(String[] args)</div>

<div><span style="white-space:pre-wrap">	</span>         {</div><div><span style="white-space:pre-wrap">		</span>          System.out.println(&quot;Hello world this is important&quot;);</div>
<div><span style="white-space:pre-wrap">	</span>         }</div><div>         }</div></div><div><br></div><div>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. </div>

<div><br></div><div>Any help or pointer is appreciated!</div><div>Thanks y&#39;all!</div><div>VJ.</div><div><br></div>
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