[Apologies for my previous email : finger slippage meant I sent before
completing the email]


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 I¹ve
misunderstood something, and unfortunately most examples come from earlier
versions 

Here is my job_conf.xml file ‹ this is just a temporary file while I set
things up. My intention is to run clustalw on our cluster using the torque
queue WitsLong, assuming our torque server is galaxy.bioinf.wits.ac.za

Below that is the output I get in the log. From the torque log it complains
that there is no default queue specified.


Any help would  be appreciated.

Thanks

Scott



<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it
is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
    <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner"/>
    <plugin id="pbs" type="runner"
load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
</plugins>
<handlers default="handlers">
        <handler id="main" tags="handlers,pbs"/>
</handlers>
<destinations default="WitsLong">
    <destination id="local" runner="local"/>
    <destination id="WitsLong" runner="pbs">
        <param id="Resource_List">walltime=72:00:00,nodes=1:ppn=8</param>
        <param id="-p">128</param>
    </destination>
</destinations>
<tools>
   <tool id="foo" handler="trackster_handler">
       <param id="source">trackster</param>
   </tool>
   <tool id="clustalw" destination="WitsLong"/>
</tools>
</job_conf>

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=9752b387803d3e1
e" "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=9752b387803d3e1
e" "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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