I'm sorry for the late response to this - I don't have any great advice regarding debugging these tool_dependencies.xml issues. I think those virtualenv tags are particularly brittle and I recommend switching to a more manual approach to Python dependencies if you are going to continue using tool_dependencies.xml - setting up packages for each Python package and referencing them the way say Macs2 does https://github.com/galaxyproject/tools-iuc/blob/master/tools/macs2/tool_dependencies.xml.

That said - the IUC and devteam have stopped writing tool_dependencies.xml files and have switch to Conda for all of our packaging. There is some documentation here:


Conda dependencies should be a bit more transparent - at least during this development stage.


On Thu, Dec 22, 2016 at 2:36 AM, Linda Bakker <linda.bakker@wur.nl> wrote:
Hi All,

I am having some problems with my tool dependencies to setup a python venv.

Dependencies.xml looks like this:

When i install my tool from the toolshed, it fails to install the venv dependency with this error message:

I am not sure what the problem exactly seems to be. os.py should be a default python package right or do i need to specify it in the dependencies file?
Can someone point me in the right direction of what the problem might be.


with regards ,
 Linda Bakker

Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bakker@wur.nl

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