Dear dev

I would  be grateful for some assistance in setting up our galaxy server to submit jobs to our torque server.. We are using release_2013.04.01

I have tried going through the install information but clearly I’ve misunderstood something, and unfortunately most examples come from earlier versions



galaxy.jobs DEBUG 2013-04-30 15:28:13,481 (33) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/33
galaxy.jobs.handler DEBUG 2013-04-30 15:28:13,527 (33) Dispatching to pbs runner
146.141.75.218, 146.141.1.81 - - [30/Apr/2013:15:28:12 +0200] "POST /galaxy/tool_runner/index HTTP/1.1" 200 - "http://galaxy.bioinf.wits.ac.za/galaxy/tool_runner/rerun?id=9752b387803d3e1e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs DEBUG 2013-04-30 15:28:14,213 (33) Persisting job destination (destination id: WitsLong)
Exception AssertionError: AssertionError('State <sqlalchemy.orm.state.InstanceState object at 0x7f79682e5150> is not present in this identity map',) in <bound method InstanceState._cleanup of <sqlalchemy.orm.state.InstanceState object at 0x7f79682e5150>> ignored
galaxy.jobs.handler INFO 2013-04-30 15:28:14,522 (33) Job dispatched
galaxy.tools DEBUG 2013-04-30 15:28:15,189 Building dependency shell command for dependency 'clustalw2'
galaxy.tools WARNING 2013-04-30 15:28:15,192 Failed to resolve dependency on 'clustalw2', ignoring
galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:15,957 (33) submitting file /home/galaxy/galaxy-dist/database/pbs/33.sh
galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:15,958 (33) command is: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/home/galaxy/galaxy-dist/database/files/000/dataset_2.dat" -o "/home/galaxy/galaxy-dist/database/files/000/dataset_60.dat" -s "ALIGNED" -l "/home/galaxy/galaxy-dist/database/files/000/dataset_61.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL"
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:15,963 (33) pbs_submit failed (try 1/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs DEBUG 2013-04-30 15:28:16,400 (34) Working directory for job is: /home/galaxy/galaxy-dist/database/job_working_directory/000/34
galaxy.jobs.handler DEBUG 2013-04-30 15:28:16,416 (34) Dispatching to pbs runner
146.141.75.218, 146.141.1.81 - - [30/Apr/2013:15:28:13 +0200] "POST /galaxy/tool_runner/index HTTP/1.1" 200 - "http://galaxy.bioinf.wits.ac.za/galaxy/tool_runner/rerun?id=9752b387803d3e1e" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs DEBUG 2013-04-30 15:28:16,668 (34) Persisting job destination (destination id: WitsLong)
galaxy.jobs.handler INFO 2013-04-30 15:28:16,689 (34) Job dispatched
galaxy.tools DEBUG 2013-04-30 15:28:16,937 Building dependency shell command for dependency 'clustalw2'
galaxy.tools WARNING 2013-04-30 15:28:16,938 Failed to resolve dependency on 'clustalw2', ignoring
galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:17,160 (34) submitting file /home/galaxy/galaxy-dist/database/pbs/34.sh
galaxy.jobs.runners.pbs DEBUG 2013-04-30 15:28:17,161 (34) command is: python /home/galaxy/galaxy-dist/tools/rgenetics/rgClustalw.py -i "/home/galaxy/galaxy-dist/database/files/000/dataset_2.dat" -o "/home/galaxy/galaxy-dist/database/files/000/dataset_62.dat" -s "ALIGNED" -l "/home/galaxy/galaxy-dist/database/files/000/dataset_63.dat" -t "Clustal_run" -d "DNA" -f "CLUSTAL"
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:17,162 (34) pbs_submit failed (try 1/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:17,971 (33) pbs_submit failed (try 2/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:19,166 (34) pbs_submit failed (try 2/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:19,975 (33) pbs_submit failed (try 3/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:21,170 (34) pbs_submit failed (try 3/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:21,978 (33) pbs_submit failed (try 4/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:23,173 (34) pbs_submit failed (try 4/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:23,982 (33) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs WARNING 2013-04-30 15:28:25,176 (34) pbs_submit failed (try 5/5), PBS error 15039: Route rejected by all destinations
galaxy.jobs.runners.pbs ERROR 2013-04-30 15:28:25,984 (33) All attempts to submit job failed
galaxy.jobs.runners.pbs ERROR 2013-04-30 15:28:27,179 (34) All attempts to submit job failed

 
 


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