On Thu, Mar 3, 2016 at 9:14 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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:
>
> https://docs.galaxyproject.org/en/master/releases/16.01_announce.html
>
> Nate (CC'd) can explain further I think.

I filed this specific issue on GitHub,
https://github.com/galaxyproject/galaxy/issues/1845

An example of the pip upgrade warning:

$ ./run.sh
...
You are using pip version 8.0.2+gx2, however version 8.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
...


Peter
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