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: pbs".
We appreciate very much for your kind help.
Le-Shin
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