They are not using a Tool Shed, so I expect that is the problem.
Tony

On Mon, Oct 26, 2015 at 12:41 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> On Mon, Oct 26, 2015 at 4:37 PM, Tony Schreiner
> <anthony.schrei...@bc.edu> wrote:
> > I take it the tool_dependencies.xml file goes in the same directory as
> the
> > custom tool xml files are. And as such applies to any of them in this
> > folder?
> >
> > Thanks
> > Tony
>
> They need to be in the same tar-ball when the tool is uploaded to
> the Tool Shed, by convention in the same folder as the tool XML
> file(s), yes.
>
> However, if you are not using the Tool Shed and simply install
> your tools manually into Galaxy then I'm not 100% sure if you
> can trigger the env.sh files via the requirement tag in the tool:
>
> <requirements>
>   <requirement type="package" version="1.66">biopython</requirement>
> </requirements>
>
> Hopefully one of the Galaxy team can clarify...
>
> For local development and deployment outside the Tool Shed,
> I always installed the dependencies myself at system level, or
> at the Galaxy Linux user level.
>
> Peter
>
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