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 ...