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[galaxy-dev] How to configure samtools in galaxy on cluster


Montag, 6. August 2012 19:39


michael xu (michael040...@gmail.com)

Recently, I am trying to configure our galaxy on our cluster with PBS 
I run galaxy locally very well on the head node, but I met one issue when I 
tried to configure galaxy on our cluster.
In universe_wsgi.ini file, I added the following entries,
start_job_runners = pbs
default_cluster_job_runner = pbs:///

And then I run the command to generate an egg,
LIBTORQUE_DIR=/usr/lib64/libtorque python scripts/scramble.py -e pbs_python 

Then I run galaxy and submitted two jobs into the PBS queue. I checked the 
galaxy log and PBS queue and found these two jobs were submitted successfully.
But after a while, galaxy told me that the two jobs were failed.

I suspected I did not modify the galaxy:tool_runners section in the 
universe_wsgi.ini file. The node machines cannot find the 3rd party tools.

Can anyone give me some advices?

Thanks a lot!

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