Hi!
This might be helpful: http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
[galaxy-dev] How to configure samtools in galaxy on cluster
Sent:
Montag, 6. August 2012 19:39
From:
michael xu (michael040525@gmail.com)
Recently, I am trying to configure our galaxy on our cluster with PBS submission. 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 --config=universe_wsgi.ini
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!