Re: [galaxy-dev] Check running jobs

2017-01-30 Thread Katherine Beaulieu 
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 
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
>  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
>
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[galaxy-dev] Vote for the Training you would like to see at GCC2017

2017-01-30 Thread Dave Clements 
Hello potential GCC2017 Attendees!

The 2017 Galaxy Community Conference (GCC2017)
 will be held 26-30 June, in
Montpellier, France.  GCC2017 training  will
be held 27-28 June.  *We need your vote to determine what to offer at
GCC2017 training.*

If there is even a remote chance that you will attend GCC2017 (it's in the
South of France; it will be summer; don't let that influence your
decision), then *please vote on which of the **34 nominated topics you
would like to see offered at GCC2017.*

*Vote Now!
*

27 June will be single track and focus on how to use Galaxy for research.
28 June will have multiple tracks, and offer the full spectrum of Galaxy
training.

Vote for as many topics as you like, but please note that the more topics
you vote for, the less your vote for each single topic will count.

*Voting closes on 8 February.*  Once that happens the organisers will
scramble to confirm instructors and set a schedule.  The training schedule
will be posted before registration opens in February.

The nominated topics this year are:

   - *Using Galaxy Topic Nominations
   *
  1. Galaxy 101 - A gentle introduction to Galaxy
  
  2. Galaxy at scale
  
  3. Visualisation of BIG DATA in Galaxy
  

  4. GSuite HyperBrowser: integrative analysis of dataset collections
  across the genome and epigenome
  
  5. ChIPseq analysis using DeepTools and MACS
  
  6. RADseq Data Analysis Through STACKS on Galaxy
  
  7. RNAseq analysis in Galaxy
  
  8. Flow Cytometry Analysis with ImmPort Galaxy
  
  9. Metabolomics Analysis with Galaxy on W4M infrastructure
  
  10. How to analyze metagenomic and amplicon data in Galaxy?
  
  11. Galaxy for Proteomics
  
  12. Processing and Analysis of Hi-C data using HiCExplorer
  
  13. SNP analysis and GWAS using SNiPlay
  
  14. Small genome de novo assembly using Galaxy
  
  15. Scripting Galaxy using the API and BioBlend
  
   - *Deploying, Administering, and Extending Galaxy Topics
   *
  1. Introduction to Galaxy admin: Setting up a Galaxy instance as a
  service
  
  2. Advanced customisation of a Galaxy instance
  
  3. Advanced accelerated Galaxy admin
  
  4. How to use Galaxy Ansible Playbooks
  
  5. Testing Galaxy
  
  6. Using and deploying your application to the cloud
  
  7. Galaxy Architecture
  
  8. Writing & Publishing Galaxy Tools
  
  9. Advanced Topics in Galaxy Tool Development
  
  10. Visualisation Development in Galaxy
  
  11. Adding support for new external sources
  
  12. Conda and Containers for Tool Dependencies - A Developers
  Perspective
  
  13. Conda and Containers for Tool Dependencies - A Deployers
  Perspective
  
  14. Introduction to Galaxy Interactive