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:


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