Great! Thanks James, this is exactly what I need.
On Wed, Nov 16, 2011 at 2:20 PM, James Taylor james@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.