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 ...
