On Dec 19, 2011, at 4:17 PM, Le-Shin Wu wrote:

Nate,

Thanks a lot for your information. After checking the log file, I found the following error message:

galaxy.jobs ERROR 2011-12-19 16:01:33,648 Job runner is not loadable: galaxy.jobs.runners.'pbs' Traceback (most recent call last): File "/N/soft/mason/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1120, in _load_plugin module = __import__( module_name ) ImportError: No module named 'pbs'

Oh, sorry I missed it the first time around. You'll need to remove the single quotes from around pbs in universe_wsgi.ini. --nate

So it looks like pbs module is not loaded. We do have pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg under galaxy-dist/eggs, but , based on the log file, it seems not within the python path. Could you please let us know how to add this egg file to the python path in galaxy?

Le-Shin

On Dec 19, 2011, at 3:51 PM, Nate Coraor wrote:

...

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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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