Hi Paul,
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
On Sep 4, 2012, at 6:25 AM, Paul-Michael Agapow wrote:
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?
Admittedly the documentation is lighter on this sort of setup, but I've been
able to puzzle it out until getting to the issue of toolsheds. We have a
large number of custom tools we want to install from our own toolshed and
the main Galaxy one. The problem: I'm not clear on how this supposed to work.
Once I started installing tools, of course they all appeared in the front-end
toolshed and are running on the front-end. Understandable - but not what I
wanted. Does this mean that for every custom tool I install, I have to go to
every Galaxy instance (frontend and job-runners) and install the tools into
their toolshed? It would seem so, but this seems ... awkward.
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.
Keep in mind that if you are, in fact, running a single Galaxy instance with
multiple web front-ends, automatically installing a tool into that galaxy
instance from the tool shed will result in displaying the tool only in the web
front-end in which it was installed. Your Galaxy server will need to be
stopped and restarted in order for the installed tools to be available in all
of the web front-ends you've configured in your Galaxy instance. Again, this
has nothing to do with any tool shed instances that you may have configured in
your Galaxy instance.
tl;dr: Toolsheds and job-ruuners - how is that supposed to work? Is there a
convenient way to handle this? Any pointers to documentation or experience?
--
Paul Agapow (p...@agapow.net)
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/