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 ...
>
> Any Idea ...
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