Hi All,
After changing the sleep in manager.py from 5 seconds to 0.2 seconds, the job 
start is very snappy.   I did not touch the various sleep(10)s that don't seem 
to be relevant.

I'm testing how long it takes to sort a short bed file in galaxy.

After the fix, the problem seems to be at the end of the process.  In the 
timeline below the gap between the job ending on the server and the client 
getting the update is 5 seconds.
Is that a built in sleep or something else? Can I turn off metadata for tools 
that don't generate it?

BTW:  thousands of seconds are on in the manager and handler logs and should be 
turned on in the main.log.

Rather than 2 round trips to the server. I think we need a special class of 
tools that run in a single round trip (like the eyeball viz). The max run time 
for this class of jobs should be no more than a few seconds. Is that is the 
roadmap somewhere?

-Robert Baertsch
UC Santa Cruz

RUN1 - 9 seconds (1 sec to start, 0.2 sec to run , 2 sec metadata, 5.5 secs to 
update client)

12:08:12.?      main: log job on main thread
12:08:12.8      manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867 
(2308) Job assigned to handler 'handler2'
12:08:13.26     handler:    start handler
12:08:13.35     handler:    job dispatched
12:08:13,44     handler:    job runner started
12:08:13,72     handler:    python tool started 
12:08:13,91     handler:           python tool finished
12:08:13,98  handler:      set_metadata.sh started
12:08:15,70  handler:    metadata ended
12:08:15,85     handler:    job Ended
12:08:21        main:      /api/histories  - update on client

RUN2 - 9 seconds (1.8 sec to start, 0.2 sec to run, 2 sec metadata, 4.5 sec to 
update client)

12:23:00.?      main: log job on main thread
12:23:00,60     manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867 
(2308) Job assigned to handler 'handler2'
12:23:01,63     handler:    start handler
12:23:01,72     handler:    job dispatched
12:23:01,81     handler:    job runner started
12:23:02,44     handler:    python tool started 
12:23:02,64     handler:           python tool finished
12:23:02,72  handler:      set_metadata.sh started
12:23:04,64 handler:    metadata ended
12:23:04,71     handler:    job Ended
12:23:09        main:      /api/histories  - update on client

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