[galaxy-user] Question about scripting

[leconte]

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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[galaxy-user] hello Newbie questions about galaxy and clustering

[leconte]

hello
  I have installed an galaxy instance for purpose testing on a 8 CPU 
server without problem all run perfectly.
  I have made some galaxy xml wrapper to understant how galaxy calls 
program and other little things.



  Now I want to install a Galaxy server with a cluster configuration.


  Before I have tested HTCondor but I have no Idea how I can mix Galaxy 
and HTCondor.


  The perfect thing was somebody have already tested this type of condor.

  But I can satisfy myself with any other cluster type.

  What I don't understant in fact ( maybe my worst problem ) where lie 
all parts of this puzzle.


 I explain.

  I know that I need Galaxy. I know too I need a cluster  ( in my case 
HTCondor )
  I understand  I need something between these 2 parts ... I think 
something like PBS or SGE but it's not totaly clear for me


I'm search on galaxy mailling list archive ... but I just found 2 mails 
in 2008 :(


has anybody made this conf or have a configuration ?

greetings

PS : sorry for my poor english :)
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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please use the interface at:

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To search Galaxy mailing lists use the unified search at:

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