On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker <linda.bak...@wur.nl> wrote:
> Hi Guys,
> So i updated my galaxy instance to release_16.01
> I usually started galaxy in a venv and used pip to install any packages my
> tool needed. (in this case, numpy and scipy)
> ...
> (.venv)@server:/galaxy-dist$ ./run.sh
> Activating virtualenv at .venv
> Ignoring indexes: https://pypi.python.org/simple
> Collecting pip==8.0.2+gx2
>   Downloading
> https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl
> (1.2MB)
>     100% |████████████████████████████████| 1.2MB 339kB/s
> Installing collected packages: pip
>   Found existing installation: pip 8.0.3
>     Uninstalling pip-8.0.3:
>       Successfully uninstalled pip-8.0.3
> Successfully installed pip-8.0.2+gx2
> And later on i get the message that i should upgrade my pip...
> I am confused...

From what I understand from following some of the relevant issues
on GitHub, this is a side effect of Galaxy using its own modified version
of pip as of Galaxy v16.01, although this isn't clear from the release notes:


Nate (CC'd) can explain further I think.


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