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.bak...@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 <+31%20317%20480%20756> > email: linda.bak...@wur.nl > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
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