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:

  <requirement type="package" version="1.66">biopython</requirement>

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.

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