Hi Paul,

Since you are using one config file/one database, you just need to manually restart the job runner after installing tools (assuming your servers are configured correctly).

The old way of having two config files, one for the web front ends and one for the SINGLE job runner is no longer supported - now you have one config file.  If you want to have one web process and one job "runner" you just configure one process as a "Web Server" and one as both the "Job Manager" and "Job Handler" as explained in the documentation here:


This system level stuff is out of my area of expertise, so others may need to chime in if you're still having issues.

Greg Von Kuster

On Sep 5, 2012, at 5:22 AM, Paul-Michael Agapow wrote:

Thanks Greg,

In case you are not aware of it, the Galaxy tool shed wiki explains the tool shed:  http://wiki.g2.bx.psu.edu/Tool%20Shed

I am aware, thanks, although I won't exclude the possibility that I've misunderstood something ...

I've "inherited" a galaxy setup from someone (details: a contractor set it up but left it unfinished so I'm completing the job while discovering and documenting what was done). The catch: it's setup as a twin galaxy instance with one as a front-end web-server and the other as the job runner.

Just to confirm, you have set up a single Galaxy instance (with a single database on the back-end) with multiple web front-ends - is this correct?

Right - a single database with one web front-end and one job-runner. And here's a detail that I forgot and may be important ... they're on different machines. They share the db and a shared data space but are on different VMs.

The Galaxy tool shed is a separate application that has no dependencies on a Galaxy instance (and vice-versa), although a Galaxy instance and a tool shed instance can each communicate with the other, so your question is a bit confusing.  A single Galaxy tool shed can be used by any number of Galaxy instances, so if you create a repository in a tool shed instance and upload tools to it, any number of Galaxy instances will be able to access that tool shed and install the repositories from it.

Right - but setting up the toolshed is not the confusing point for me. It's how the job-runner gets to use a tool installed from a toolshed when it's on a different machine to the front-end. The tool has to be installed into the job-runner as well, right? 

As said, I inherited this system, so I'm discovering how it's been setup.


Paul Agapow (pma@agapow.net)