Looks like it's working! The problem I had run into, in hindsight, was
a) I hadn't set tool_dependency_dir as I didn't know about it
b) if I had set it, I was installing tools to
$SW/tool-name/version-number/ but the default tool wrappers in
galaxy-dist don't have version numbers set, so they will just look in
$SW/tool-name/ .

Can I suggest this be added to the wiki somewhere under the Admin
pages? Apologies if it's there, I couldn't find it except under News
Briefs at 

As well as being on the wiki it would be useful to have it (commented
out by default) in universe_wsgi.ini. I think the tool_dependency_dir
variable isn't in there at all at the moment, at least in the
galaxy-dist I have. It would also be useful to have a brief mention or
link to it on http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup to
save time for people like me who had tools installed in a non-standard

Thanks again!

On Wed, Nov 16, 2011 at 3:01 PM, Clare Sloggett <s...@unimelb.edu.au> wrote:
> 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.
> --
> E: s...@unimelb.edu.au
> P: 03 903 53357
> M: 0414 854 759

E: s...@unimelb.edu.au
P: 03 903 53357
M: 0414 854 759

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