On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:

> If this is the case, what is the best way to install and maintain two
> versions of the same tool? I can write code into the wrapper to find
> the correct version of the tool in a given case, but I was wondering
> if there is a more standard 'galaxy' way to configure this.

You should provide "tool_dependency_dir" in the config file and point it at 
some directory $SW where you will install tools under.

With this enabled, when a tool has a dependency, Galaxy will look for it under 
that directory and attempt to run a script to setup the environment. For 
example if you have tool with a dependency on foo version 1.3, Galaxy will look 


and if found will source it as part of the job submission script. This usually 
contains something simple like


to add the binaries installed with the dependency to the path.

Ideally all dependencies used by Galaxy tools would be installed in this way.
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