Hi Nate,
Ok. Looks like I *am* misunderstanding something. Scrub that last email!:-)
I was running some SAM-BAM conversions but I was getting confused since my jobs may have actually finished (and are not visible in the queue) but in the galaxy interface it is still showing it as running. So it looks like the problem may be with the our samtools config rather than more general case. More digging required...
Depending on how big those files are, setting metadata may be what's causing the lag between the actual command finishing and Galaxy marking the job as finished. You may want to set:
set_metadata_externally = True
Ok. Thanks. Will try that.
In the config to force this to happen out on the cluster.
Trying another samtool...in the Galaxy History the job is still running (yellow background), but is finished according to SGE and there appears to be some output produced. galaxy.jobs.runners.sge DEBUG 2010-04-29 15:32:26,051 (136) submitting file /wwwdata/galaxy-dist/database/pbs/galaxy_136.sh galaxy.jobs.runners.sge DEBUG 2010-04-29 15:32:26,052 (136) command is: python /wwwdata/galaxy-dist/tools/samtools/sam2interval.py --input_sam_file=/wwwdata/galaxy-dist/database/files/000/dataset_153.dat -p > /wwwdata/galaxy-dist/database/files/000/dataset_210.dat Any ideas? Steve