Hi Lionel,

> 
> I've been scratching a bit my head about how galaxy builds dependency, 
> fruitlessly so far... Here is my problem: I have a local tool (not 
> installed through a toolshed) that makes use of another tool (aragorn) 
> that I installed from the toolshed.
> 
> Aragorn requires the aragorn package, as stated in its .xml file:
> 
> <requirement type="package" version="1.2.36">aragorn</requirement>
> 
> When I run aragorn, it runs fine, and the dependencies are built fine.
> 
> galaxy.tools DEBUG 2013-09-05 12:20:14,340 Building dependency shell 
> command for dependency 'aragorn'
> 
> 
> Now when I run my tool, which has the exact same requirement line:
> 
> <requirement type="package" version="1.2.36">aragorn</requirement>
> 
> the dependency is not built correctly, and fail to resolve:
> galaxy.tools DEBUG 2013-09-05 12:26:22,823 Building dependency shell 
> command for dependency 'aragorn'
> galaxy.tools WARNING 2013-09-05 12:26:22,823 Failed to resolve 
> dependency on 'aragorn', ignoring
> 
> The required package is installed in 
> galaxy-dist/tool-dependency-dir/aragorn/1.2.36/bgruening/trna_prediction/d34f31cbc9dd/
>  
> and there is an env.sh there that points correctly to the binaries. Now 
> if I copy that env.sh file into 
> galaxy-dist/tool-dependency-dir/aragorn/1.2.36/, it works fine and the 
> dependency command is built all fine, but it is not done automatically 
> when I install aragorn through the toolshed.
> 
> Am I doing something wrong? Missing something somewhere?

You have done everything right. That functionality is currently not
implemented I guess. If you would install your tools by means of the
toolshed, the env file from aragorn will be copied automatically to a
place where your tool will find it. Without the toolshed that will not
be the case. I think one reason is, that you can have installed
different versions of aragorn from different authors. In that case your
workaround will not work.

If your tools is of interest for a wieder community, I would be happy to
integrate it into my repository (aragorn).

Cheers,
Bjoern

> Cheers,
> 
> Lionel
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