Thanks for the answer!  I&#39;ve copied this response to the dev list email instead, after realizing its probably best there.  <div><br></div><div>I&#39;m also having some trouble getting our PBS system configured.  I have pbs://hostname/ as my pbs parameter in the universe file, as well as everything else specified in the documentation.  I&#39;m getting no error in the interface, and the backend never actually gets the job.  The error I see in the logs says:</div>

<div><br></div><div><div>galaxy.jobs.runners.pbs ERROR 2009-10-30 13:40:27,762 Uncaught exception queueing job</div><div>Traceback (most recent call last):</div><div>  File &quot;/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py&quot;, line 144, in run_next</div>

<div>    self.queue_job( obj )</div><div>  File &quot;/home/perin/galaxy-dist/lib/galaxy/jobs/runners/pbs.py&quot;, line 219, in queue_job</div><div>    script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, &quot; &quot;.join(job_wrapper.get_input_fnames() + output_fnames), self.app.config.pbs_stage_path, exec_dir, command_line)</div>

<div>TypeError: sequence item 1: expected string, DatasetPath found</div><div><br></div><div><br></div><div>I&#39;m guessing this has something to do with my config parameters, and the queue its trying to submit to.  the pbs://hostname/ value was used under the assumption that it would default to the &#39;default&#39; queue on our cluster, so I&#39;m wondering if I need to hard code those values into the connection string?  I&#39;m a little confused as to how the syntax translates to the actual required string.  My guess is, for our values:</div>

<div><br></div><div>pbs://<a href="http://variome.chop.edu/default">variome.chop.edu/default</a>  </div><div><br></div><div>Perhaps its related to the scrambling of the egg instead?  I simply passed LIBTORQUE_DIR to the directory containing my libtorqure.so etc... </div>

<div><br></div><div>?  Thanks in advance.</div><div><br></div><div>Juan Perin </div><div><br></div><div><br></div><div><br></div><div class="gmail_quote">On Fri, Oct 30, 2009 at 12:07 PM, Nate Coraor <span dir="ltr">&lt;<a href="mailto:nate@bx.psu.edu">nate@bx.psu.edu</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">Juan Perin wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I&#39;m hosting galaxy locally and am trying to figure out how to change  the temporary upload location of files from the root / /tmp folder to  something else.  My /tmp partition is too small to handle large fastq  files and this is causing me problems.  I see where to change things  in the universe file, but that&#39;s the final location, not the temporary  space.<br>


</blockquote>
<br></div>
Hi Juan,<br>
<br>
A quick solution is to set $TEMP in your shell environment.  In the future, we&#39;ll force uploads to honor new_file_path in universe_wsgi.ini.<br><font color="#888888">
<br>
--nate<br>
</font></blockquote></div><br></div>