On Dec 19, 2011, at 4:17 PM, Le-Shin Wu wrote:
> 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:
> Traceback (most recent call last):
> File "/N/soft/mason/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1120, in
> 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.
> 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?
> 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
>>> <tool id="mytool" name="Testing tool" version="0.12.7">
>>> <description>do the pbs testing</description>
>>> /N/soft/mason/test_tool -p 8 hg18 -f $inputseq $output
>>> <param name="db" type="inputseq" label="input file" />
>>> <data format="sam" name="output" label="result" />
>>> <param name="inputseq" value="a.fa" />
>>> <output name="output" file="b.sam" />
>>> **What it does**
>>> This tool uses Bowtie to produce an alignment.
>>> .. _Bowtie: http:
>>> 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" />
>>> (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.
>>> We appreciate very much for your kind help.
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