Use qrsh instead of qsub to submit the job should help, I believe.<br><br><div class="gmail_quote">On Tue, Apr 5, 2011 at 10:27 AM, andrew stewart <span dir="ltr">&lt;<a href="mailto:andrew.c.stewart@gmail.com">andrew.c.stewart@gmail.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">I&#39;m aware of how to configure Galaxy to use SGE in universe_wsgi.ini, however what I want to do is a little different.  Because I only want certain processes to be submitted to the queue, I&#39;d rather control this at the tool configuration level (the xml wrapper).  For example:<div>

<br></div><div>&lt;command interpreter=&quot;bash&quot;&gt; </div><div>    qsub myscript.sh</div><div>&lt;/command&gt;</div><div><br></div><div>This will work, except that the status of the job (in Galaxy) shows as completed even though the job has simply been submitted to SGE.  Basically Galaxy &#39;loses track&#39; of the process because the submission process (myscript.sh) has completed even if the actual job hasn&#39;t.  </div>

<div><br></div><div>Has anyone else tried anything like this before, or have anything helpful to suggest?  One thought is to somehow cause the myscript.sh process to pause until the SGE job has completed... somehow.</div>

<div><br></div><div>Any advice appreciated.</div><div><br></div><div>Thanks,</div><div>Andrew</div>
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