'qstat -f | grep jobname' will give you the full jobname without truncation. Personally, I think the qstat reporting gives too little information. I've written a perl script to parse the output of qstat -f to give a bit more information. So truncation of jobnames for qstat shouldn't be an issue.
On Fri, Feb 3, 2012 at 5:40 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > Hello all, > > We're not planning to try the new "run cluster jobs as user" > functionality (at least, not just yet), so for now all our SGE jobs > show on the cluster via qstat or any other monitoring tool as > belonging to the user "galaxy". > > Currently the jobs are submitted as shell scripts "galaxy_NNN.sh" > where NNN is the Galaxy job number. This is almost no help at > all for a cluster administrator to use for monitoring or diagnostics. > Given qstat truncates the command to 10 letters anyway, I > typically see things like "galaxy_42." for "galaxy_42.sh" so > once job numbers exceed three digits it becomes ambiguous. > > To me there are three things that could be done with the script > name which would make it far more instructive in this regard. > > First, move the job number nearer the start. I'd find just > "gNNN.sh" more useful than "galaxy_NNN.sh" simply > because of the truncation in qstat. > > Second, unless configured to "run jobs as the user", then > include the user name. I would suggest the Galaxy user's > "Public Name" (which Galaxy should ensure avoids potential > problem characters in filenames) or perhaps the pre- > domain part of their email address? e.g. "gNNN_USER.sh" > > Third, the Galaxy tool ID (which will contain dashes and > underscores, but no spaces etc). e.g. "gNNN_TOOL.sh" > Even with truncation, this would make it easy to tell NCBI > BLAST jobs apart from TopHat or whatever. > > Obviously using both, e.g. "gNNN_USER_TOOL.sh" > wouldn't work so well with the truncation in qstat, but > you should still see enough of the username to make > it informative. > > Does this make sense? It would seem to be a small > tweak needed in lib/galaxy/jobs/runners/drmma.py > where there is currently also a hard coded path bug: > https://bitbucket.org/galaxy/galaxy-central/issue/715/ > > Regards, > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
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