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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