Hi, Thon <div>I&#39;m guessing here: but now that bwa is kept in the toolshed, the tool name appears to be <a href="http://toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3" target="_blank" style="font-family:arial,sans-serif;font-size:12px;line-height:16px">toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3</a> according to your job runner entry - so I wonder if that whole ugly string now needs to be in the tool_runners section to over-ride the default rather thant &quot;bwa_wrapper&quot; ? </div>
<div><br></div><div>This might be an unforseen consequence of the way the toolshed adapts tool names to keep versions under control. Fixing this might be a little tricky since one goal is to keep multiple tool versions separate - but we will all want all versions of bwa_wrapper to use the same runner flags?</div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Dec 6, 2012 at 8:40 AM, Anthonius deBoer <span dir="ltr">&lt;<a href="mailto:thondeboer@me.com" target="_blank">thondeboer@me.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div>Hi,</div><div><br></div><div>In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...</div>
<div><br></div><div>This is the setting for bwa_wrapper in my universe_wsgi.ini:</div><div><br></div><div>bwa_wrapper = drmaa://-V -q long.q -pe smp 4/</div><div><br></div><div>and this is what the job admin page shows:</div>
<div><br></div><div>It&#39;s in a different queue and does not use the smp setting I ask for...(It&#39;s the default setting)</div><div><br></div><div><br></div><div><br></div><div>any ideas?</div><div><br></div><div><br>
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<tbody><tr><td style="padding:5px">7</td><td style="padding:5px">X</td><td style="padding:5px">26 minutes ago</td><td style="padding:5px"><a href="http://toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3" target="_blank">toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3</a></td>
<td style="padding:5px">running</td><td style="padding:5px">python /mnt/ngs/analysis/svcgalaxy/shed_tools/<a href="http://toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py" target="_blank">toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/bwa_wrapper.py</a> --threads=&quot;4&quot; --fileSource=indexed --ref=&quot;/mnt/ngs/analysis/svcgalaxy/DATA/galaxy-indexes/bwa-indexes/human_g1k_v37_decoy.fasta&quot; --do_not_build_index --input1=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R1.fastq --input2=/home/tdeboer/P/MUT190-MAIN/fastq-2_205/2_205_1_AAACAT_R2.fastq --output=/mnt/ngs/analysis/svcgalaxy/DATA/files/000/dataset_776.dat --genAlignType=paired --params=pre_set --suppressHeader=false</td>
<td style="padding:5px">drmaa://-V -q all.q -pe smp 1/</td><td style="padding:5px">4440144</td></tr></tbody></table></div></div></blockquote></div><br>
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