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:

- https://docs.galaxyproject.org/en/latest/admin/conda_faq.html

- http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda

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

-John

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.

Thanks!

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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