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.Dooley@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.