Ok so there is no way to access the galaxy object outside of galaxy? I'm looking for something like the 'trans' variable often seen throughout the Galaxy code base so that I can use sqlalchemy and make a database query. Thanks for replying. Katherine On Fri, Jan 27, 2017 at 5:40 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Hi Katherine,

I don't think Galaxy itself will tell you this, in part because the details would be dependent on the Cluster being used.

I would do that via whatever cluster management system you are running (e.g. qstat or qmon if using SGE).

By default all the jobs will be submitted by the Galaxy user account, but if you are submitting jobs as the individual users then you can still spot Galaxy jobs via their naming convention (starting "g", number, underscore, ..., tool name, user's email).

Peter

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Hi there, We are trying to build our own Galaxy cluster and I was wondering if

On Thu, Jan 26, 2017 at 6:58 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote: there

...

was a way to check if there are any running Galaxy jobs on a specific server? This would be to determine whether or not to remove the server from the cluster. Thanks! Katherine

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I think this is a bit more complicated than what I am looking for. All I am looking for is a way to get the result of this query:

jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, or_( trans.app.model.Job.state == trans.app.model.Job.states.NEW,

trans.app.model.Job.state == trans.app.model.Job.states.QUEUED,

trans.app.model.Job.state == trans.app.model.Job.states.RUNNING,

trans.app.model.Job.state == trans.app.model.Job.states.UPLOAD ) ) ) \ .order_by( trans.app.model.Job.table.c.update_time.desc() ).all()

from the file /lib/galaxy/web/base/controllers/admin.py, without having to use the UI. Has anyone done something like this before? On Fri, Jan 27, 2017 at 10:03 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Ah - I assumed you meant from the user-facing UI, or the reports page.

I would suggest exploring the advance job metrics options, see e.g.

https://github.com/galaxyproject/galaxy/blob/dev/ config/job_metrics_conf.xml.sample

I've never used it, but perhaps the backend using Collectl (http://collectl.sourceforge.net/) would cover this?

Peter

On Fri, Jan 27, 2017 at 2:50 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:

...

Ok so there is no way to access the galaxy object outside of galaxy? I'm looking for something like the 'trans' variable often seen throughout the Galaxy code base so that I can use sqlalchemy and make a database query. Thanks for replying. Katherine