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Configuring Torque and InterProScan

10 Jul
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If by the chance, you want to use InterProScan with Torque Resource Manager (queueing system based on PBS project) it doesn’t work by default (it’s tested with LSF, configuration files are supplied for original PBS and Sun Grid Engine). Fortunately there are two small changes needed in the InterProScan config files to make it work. First, during iprscan configuration, choose PBS54 as your queueing system. Then, in the file pbs54.conf (IPRSCANHOME/conf) remove “-d” switch from following two lines:

asyncsub=qsub [%optqueue][%optresource] -d -o /dev/null -e /dev/null "[%toolcmd]"
syncsub=qsub [%optqueue][%optresource] -d -o /dev/null -e /dev/null -I "[%toolcmd"]

Assumming that Torque binaries are available in the global PATH (qsub, qdel etc., on my machine they sit under /usr/local/bin), change in default shell in the enviroment file pbs54env.sh – from #!/bin/sh to #!/bin/bash. Also, you can add another directories to the PATH in that file (I didn’t). Voilla. InterProScan jobs are now queued.

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3 Comments

Posted by on July 10, 2008 in bioinformatics, Software

 

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3 responses to “Configuring Torque and InterProScan

  1. nsaunders

    July 10, 2008 at 23:01

    Good to see this getting some publicity. I wrote some notes on using iprscan with PBS at the Nodalpoint wiki a few years ago.

     
  2. Pawel Szczesny

    July 11, 2008 at 01:28

    Thanks Neil, your notes would save me time and this post wouldn’t even appear if I searched for “OpenPBS iprscan” (the Nodalpoint wiki page comes fourth) not “Torque iprscan”. Web 3.0, where are you?

     
  3. Sarah Hunter

    August 26, 2008 at 15:21

    Hi,

    Thanks for this info – I’m going to add it to the FAQs for the next release (coming very very soon). Note that the “-l resource” bug has now been fixed.

    Also note that we have a new version of InterProScan in development (v5). We plan on making this a bit more “open source” than the current version. If you would like more information, please email interhelp (at) ebi.ac.uk

    Many thanks for your input into the project. If anyone has any feedback or questions, please contact EBI support on http://www.ebi.ac.uk/support/

    Cheers,

    Sarah Hunter

     
 
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