Great! Thanks James, this is exactly what I need.

On Wed, Nov 16, 2011 at 2:20 PM, James Taylor <ja...@jamestaylor.org> wrote:
> 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 for:
>
>        $SW/foo/1.3/env.sh
>
> and if found will source it as part of the job submission script. This 
> usually contains something simple like
>
>        PATH=$PACKAGE_BASE/bin:$PATH
>
> 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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