Hello Nicolas,

On Nov 22, 2011, at 11:04 AM, Nicolas Delhomme wrote:

> Hi Greg,
> 
> I've been scanning the mailing list, but wasn't lucky enough to find the 
> answer I was looking for.
> 
> Basically, we would be interested to have our own Galaxy Tool Shed in-house, 
> to develop and test tools within our local Galaxy instance. What I'm thinking 
> of, is to use the power of the tool shed to develop new algorithm, new tools, 
> etc. that could be published afterwards.


This is great, but keep in mind that the intent of the tool shed (whether it is 
a local, proprietary tool shed or the public Galaxy tool shed) is to provide a 
vehicle for sharing tools (and tool-related objects like workflows, data types, 
etc) that are determined to be functional within a Galaxy instance.  So the 
primary use of a tool shed should be to enable sharing.  The tools themselves 
should be implemented within a development environment that includes a Galaxy 
instance, and when a tool is deemed functional, it can then be uploaded to the 
tool shed for sharing.

You can, however, tweak the primary intent of a tool shed to meet your needs.  
In your case, it seems that you may be interested in using a local tool shed 
instance to share tools between developers during the development process.  If 
this is the case, then your approach can be one where a developer creates a 
repository on the local tool shed multiple developers can clone it.  The 
mercurial command line process for committing, pushing, pulling and updating 
can be used to share updates to the tool code by multiple developers throughout 
the process.

If a single developer is implementing the tool however, it may make more sense 
to not use the tool shed as part of the development process - just upload the 
tool when it is functional.


> Because these would be sensitive material, we would not want to put them 
> right away on the public test Tool Shed. Having a local Tool Shed instance 
> would still be very helpful in releasing these tools to the community 
> afterwards, as they would have been integrated and developed within that 
> framework from the start. 

This is a good approach.

> 
> Any pointers on how to achieve this are welcome as I'm not so familiar with 
> the Tool Shed yet, e.g. would making a local clone of the tool shed 
> repository be enough?

Make sure to read the tool shed wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed.  
I make sure to keep this up-to-date with the latest features of the tool shed.  
You'll ffind, however, that there are some tool shed admin user features that 
have not yet been documented.  If you have any question, let me know.

The tool shed is included in the Galaxy distribution, so no additional cloning 
is necessary - it is just a different webpp from Galaxy itself.  It uses a 
different database from Galaxy, which you configure in the file 
community_wsgi.ini (the equivalent of universe_wsgi.ini for Galxy).  After you 
have the configuration settings as you want them, start up your local tool shed 
by:

%sh run_community.sh

Feel free to ask questions!


> 
> Thanks,
> 
> Nico
> 
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> Genome Biology Computational Support
> 
> European Molecular Biology Laboratory
> 
> Tel: +49 6221 387 8310
> Email: nicolas.delho...@embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
> 
> 
> 
> 
> 
> 
> ___________________________________________________________
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




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