On Dec 19, 2011, at 3:03 PM, Le-Shin Wu wrote:

> We are trying to get galaxy to work on our cluster. Unfortunately, there are 
> some questions I still cannot find the answer to and I'm hoping someone here 
> can help me out. 
> 
> We would like to use the unified approach with TPRQUE PBS to support running 
> galaxy tools on a cluster. Our questions are listed as below.
> 
> (1) How to configure the universe_wsgi.ini file? Based on the galaxy wiki 
> page, we changed the following parameters in universe_wsgi.ini
>      new_file_path =  /N/dc/projects/galaxy/new_files # this directory is 
> accessible both to galaxy server and cluster nodes
>      start_job_runners = 'pbs'
>      default_cluster_job_runner =  pbs://cluster.hostname.edu/ 
> #cluster.hostname.edu is the hostname for our cluster
> 
>     Also under [galaxy:tool_runners] section, we add a new tool named mytool 
> for testing as below.
>     mytool = pbs://cluster.hostname.edu/ 
> 
>     Does this configuration look correct and enough?
> 
> (2) We created a new python egg for pbs by using
>      LIBTORQUE_DIR=/usr/local/lib/libtorque python scripts/scramble.py -e 
> pbs_python --config=universe_wsgi.ini
> 
>      A new file pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg was then created 
> under eggs. 
> 
>      Do we need to do other things or only this operation is enough?
> 
> (3) We created a new directory named mytool under  tools and added a new file 
> named newTool.xml in it. The content of newTool.xml is as below. Note that, 
> the /N/soft/mason/test_tool is a executable binary file at our cluster. 
> 
> <tool id="mytool" name="Testing tool" version="0.12.7">
>  <description>do the pbs testing</description>
>  <command>
>      /N/soft/mason/test_tool -p 8 hg18 -f $inputseq $output
>  </command>
>  <inputs>
>     <param name="db" type="inputseq"  label="input file" />
>     </inputs>
>  <outputs>
>    <data format="sam" name="output" label="result" />
>  </outputs>
> <tests>
> <test>
>      <param name="inputseq" value="a.fa"  />
>      <output name="output" file="b.sam"  />
> 
>    </test>
>  </tests>
> 
>  <help>
>      **What it does**
>           This tool uses Bowtie to produce an alignment.
>     .. _Bowtie: http:
> 
>  </help>
> </tool>
> 
> Does this xml file look correct? Do we also need a python wrapper file to 
> somehow invoking PBS support?
> 
> (4) Add the following text into tool_conf.xml.
>     <section name="My Tools" id="mt">
>          <tool file="mytool/newTool.xml" />
>     </section>
> 
> (5) After doing the above modification and restarting our galaxy server , we 
> can see "My Tools" showing on the tools panel of our galaxy web interface. 
> But after we select an input file and click execute button, the job status 
> shows an error "Unable to run job due to a misconfiguration of the Galaxy job 
> running system.  Please contact a site administrator". We also check the log 
> file, it shows " Invalid job runner: bps".

Hi Le-Shin,

It would appear that the PBS job runner failed to start.  You should be able to 
see a traceback with more details about this displayed during the server's 
startup.

--nate

> 
> We appreciate very much for your kind help.
> 
> 
> Le-Shin  
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