Hmmm... you know what.  I tested this out and it looks like Galaxy expects
the git repo to be named the same as the package name in your tool
dependencies file ffp-phylogeny.  If you change the git command to:

git clone https://github.com/apetkau/ffp-3.19-custom.git *ffp-phylogeny*

I think it should work.

Aaron


On Fri, Aug 1, 2014 at 2:09 PM, Dooley, Damion <damion.doo...@bccdc.ca>
wrote:

> A little more info:
>
> <action type="shell_command">ls -a</action>
>
> #############################################
> ls -a
> STDOUT
> .
> ..
> #############################################
>
> #############################################
> ls -a
> STDERR
>
> so I guess the .git archive is being unpackaged somewhere else!  After
> lunch I'll return to explore this mysterious territory.
>
> d.
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