Hello,

I've moved this over to the galaxy-dev list since it concerns a local installation.

You'll want to use the 'condor' job running plugin, which is provided with the Galaxy distribution. Have a look at the job_conf.xml.sample_advanced file to see how this would be configured.

A very basic job_conf.xml that should submit all jobs to HTCondor:

<?xml version="1.0"?> <job_conf> <plugins workers="4"> <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> </plugins> <destinations default="condor"> <destination id="condor" runner="condor"/> </destinations> </job_conf>

--nate

On Apr 19, 2013, at 8:32 AM, leconte wrote:

hello,

My subject is at the border between Galaxy and Condor

I'found method to use Galaxy with condor cluster solution.

In fact I have wrote a script when Galaxy call clustalw2 , it calls in fact a script called clustalw2.

All run exactly as I want excepting ... but Galaxy get in error and said there was a problem

I turn my script to debug mode and it puts followings output

• prog=/usr/bin/clustalw2
• err=0
• infile=-infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
• outfile=-outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat
• outorder=-OUTORDER=ALIGNED
• seqnos=-SEQNOS=OFF
• typeseq=-TYPE=DNA
• var6=
• var7=
• var8=
• var9=
• echo

++ echo -infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat ++ sed -e s/-infile=//

• infile2=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat

++ sed -e 's/galaxy_dataset_(.*).dat//' ++ sed -e s/-outfile=// ++ echo -outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat

• WorkingDir=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/
• mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/
• mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/
• mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/
• [[ -n /usr/bin/clustalw2==clustalw2 ]]
• echo 'universe = vanilla'
• echo 'executable = /usr/bin/mpirun '
• echo 'arguments = "-np 10 -hostfile /home/galaxy/hostfile /usr/bin/clustalw-mpi -infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat -outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat -OUTORDER=ALIGNED -SEQNOS=OFF -TYPE=DNA "'
• echo 'Getenv = True

machine_count = 1 transfer_input_files = /home/galaxy/hostfile,/usr/bin/clustalw-mpi, /home/galaxy/galaxy-dist/database/files/000/dataset_11.dat should_transfer_files = yes Log = /home/galaxy/logs/normal.$(cluster).$(process).log Output = /home/galaxy/logs/normal.$(cluster).$(process).out Error = /home/galaxy/logs/normal.$(cluster).$(process).error notification = never queue 1'

• /usr/bin/condor_submit /home/galaxy/submit

Submitting job(s). 1 job(s) submitted to cluster 179.

I suspect the method I use, doesn't return properly information to galaxy ... but I don't know what I can do ...

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