I&#39;m building a pipeline which, initially, will use some existing tools and then I plan on adding some of my own.  In running this though I&#39;ve run into a few questions that might have to do with how Galaxy in general works rather than being tool-specific.<div>
<br></div><div>I&#39;ve made it up to running Realigner Target Creator (part of GATK tools) and I don&#39;t see a convention of specifying what version of GATK it expects to be installed.  Then, running the tool failed with &quot;<span style="color:rgb(0,0,0);white-space:pre-wrap">Running with the -et NO_ET or -et STDOUT option requires a GATK Key file.&quot;  It seems the -et option is hard-coded into the component without passing a key, which has to be applied for.  I didn&#39;t want this at all, so I modified the following file:</span></div>
<div><span style="color:rgb(0,0,0);white-space:pre-wrap"><br></span></div><div><font color="#000000"><span style="white-space:pre-wrap">galaxy-dist/tools/gatk/realigner_target_creator.xml</span></font><br></div><div><font color="#000000"><span style="white-space:pre-wrap"><br>
</span></font></div><div><font color="#000000"><span style="white-space:pre-wrap">and removed the following line:</span></font></div><div><font color="#000000"><span style="white-space:pre-wrap"><br></span></font></div><div>
<font color="#000000"><span style="white-space:pre-wrap">-et &quot;NO_ET&quot; ##ET no phone home</span><br></font></div><div><font color="#000000"><span style="white-space:pre-wrap"><br></span></font></div><div><font color="#000000"><span style="white-space:pre-wrap">Then I added the component and tried to run again, still getting the same error.  If I removed that line how is it still part of the call?  Is Galaxy caching the xml tool files?  Also, is there a way to see the precise commands being executed by Galaxy for any particular tool?</span></font></div>
<div><font color="#000000"><span style="white-space:pre-wrap"><br></span></font></div><div><font color="#000000"><span style="white-space:pre-wrap">Thanks -</span></font></div><div><font color="#000000"><span style="white-space:pre-wrap"><br>
</span></font></div><div><font color="#000000"><span style="white-space:pre-wrap">Joshua</span></font></div>