Hi Melissa,
The question in the title is easy to answer - most large galaxy instances
run (most) jobs on a connected cluster which is effectively 'background' I
guess so "yes - all of them on cluster backed Galaxy instances" might be a
reasonable response.

The questions in the text are more complex, but (eg) AFAIK there's no
technical reason why some batch process owned by the Galaxy user shouldn't
issue a
sh run.sh --stop-daemon
at any time to stop Galaxy. Exactly when that might be a good idea is not
so clear to me so I'm probably missing something here - the Galaxy process
doesn't consume a lot of resources and is typically left running
permanently so users can take advantage of the persistence and
reproducibility. Tools are AFAIK not generally written to launch their own
background processes because they are managed by the Galaxy job runner
which interfaces with (eg) SGE or Torque to run each separate tool
invocation and clean up when it has completed.

I'm sure you could run a transient Galaxy to batch up some workflows or
other processes and I'm sure a VM might be part of that and the API allows
a lot of automation. There's a new Galaxy docker image project which might
be even more efficient and helpful - see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019289.html



On Sat, Jun 7, 2014 at 10:18 AM, Melissa Cline <cl...@soe.ucsc.edu> wrote:

> Hi folks,
>
> We're working on developing a VM which we'd like to be tightly coordinated
> with Galaxy, such that VM users can export data from the VM into Galaxy,
> perform further analyses on that data, and then import the analysis results
> into the VM for storage (from where it will serve additional applications).
>  Right now, I'm picturing this as a set of Galaxy tools that launch the VM,
> manage the data import and export, and shut down the VM at the appropriate
> time.  Or is there a better approach I didn't consider?
>
> Assuming the answer is "no", then are there any tools in the toolshed that
> launch background processes?  If so, I'd like to look at them.
>
> And assuming that my VM will be running in the background, I'd like it to
> shut down when Galaxy shuts down.  Is there a way to configure a process to
> be run when it's time to quit Galaxy?
>
> Thanks!
>
> Melissa
>
>
>
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