thanks for your replies - yes, makes sense to edit in the workflow files. Btw I like how this structured a lot.
I have one more question: after some testing we want to dock some larger libraries now. Our sysadmin asked me that if I will submit now several thousands (similar) jobs whether I can define them as “array jobs” (our cluster uses SGE).
If I start a larger docking now (on 1000 nodes), I was planning to go with:
./vf_start_jobline.sh 1 1000 templates/template1.sge.sh submit 1
I guess this will not define array jobs but just submit 1000 jobs, right?
At least in the template1.sge.sh by default. The qsub option for an array job would be “-t”.
Could I add e.g. -t 1-100 to the options in the template? I am worried that this might produce problems further down, when new jobs are submitted etc. Maybe I just need to test this with a smaller library.
Thanks a lot & best
qsub man http://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html