Hi Ming,<div>   just an idea, &quot;-w n&quot; might be hiding the error reporting. Is your jobs getting submitted and executed correctly? </div><div><br></div><div>For the queuing , you can add &quot;galaxy&quot; at the end, makes it</div>

<div><br></div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><font class="Apple-style-span" color="#FF0000">drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/galaxy</font></span></div>

<div><font class="Apple-style-span" color="#FF0000" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; "><font class="Apple-style-span" color="#333333">here galaxy is queue name.</font></span></font></div>

<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; "><font class="Apple-style-span" color="#333333"><br></font></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; "><font class="Apple-style-span" color="#333333"><br clear="all">

</font></span></font> <br>With Regards,<br>----------------<br>Ambarish Biswas, <br>

University of Otago<br>
Department of Biochemistry,<br>Dunedin, New Zealand,<br>
Tel: +64(22)0855647<br>
Fax: +64(0)3 479 7866<br>
<br><div style="display:inline"></div><div style="display:inline"></div><div style="display:inline"></div><br>
<br><br><div class="gmail_quote">On Thu, Jul 28, 2011 at 6:21 AM, Ka Ming Nip <span dir="ltr">&lt;<a href="mailto:kmnip@bcgsc.ca">kmnip@bcgsc.ca</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

Answering myself here...<br>
<br>
I don&#39;t see the error anymore after adding &quot;-w n&quot;:<br>
<br>
[galaxy:tool_runners]<br>
...<br>
mytoolname = drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/<br>
...<br>
<br>
Is this what other Galaxy admins do when using drmaa native options for their SGE?<br>
<br>
Ka Ming<br>
________________________________________<br>
From: <a href="mailto:galaxy-dev-bounces@lists.bx.psu.edu">galaxy-dev-bounces@lists.bx.psu.edu</a> [<a href="mailto:galaxy-dev-bounces@lists.bx.psu.edu">galaxy-dev-bounces@lists.bx.psu.edu</a>] On Behalf Of Ka Ming Nip [<a href="mailto:kmnip@bcgsc.ca">kmnip@bcgsc.ca</a>]<br>


Sent: July 26, 2011 10:39 AM<br>
To: <a href="mailto:galaxy-dev@lists.bx.psu.edu">galaxy-dev@lists.bx.psu.edu</a><br>
Subject: [galaxy-dev] DRMAA options for SGE<br>
<div><div></div><div class="h5"><br>
Hi,<br>
<br>
I am trying to configure the proper memory resource requests for my Galaxy tool.<br>
This is what I have under the tool_runners section of universe_wsgi.ini<br>
<br>
[galaxy:tool_runners]<br>
...<br>
mytoolname = drmaa://-l mem_free=1G -l mem_token=1G -l h_vmem=1G/<br>
...<br>
<br>
When I execute my tool on Galaxy, I get the error below in the shell that I ran &quot;sh run.sh&quot;:<br>
<br>
galaxy.jobs.runners.drmaa ERROR 2011-07-26 09:54:01,930 Uncaught exception queueing job<br>
Traceback (most recent call last):<br>
  File &quot;/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py&quot;, line 112, in run_next<br>
    self.queue_job( obj )<br>
  File &quot;/home/kmnip/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py&quot;, line 177, in queue_job<br>
    job_id = self.ds.runJob(jt)<br>
  File &quot;/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/__init__.py&quot;, line 331, in runJob<br>
  File &quot;/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/helpers.py&quot;, line 213, in c<br>
  File &quot;/home/kmnip/galaxy/galaxy-central/eggs/drmaa-0.4b3-py2.4.egg/drmaa/errors.py&quot;, line 90, in error_check<br>
DeniedByDrmException: code 17: error: no suitable queues<br>
<br>
All the flags I used work with qsub commands on the SGE cluster I use. The tool runs<br>
when I comment out the line in universe_wsgi.ini.<br>
<br>
Thanks,<br>
Ka Ming<br>
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</div></div></blockquote></div><br></div>