On Thu, Mar 3, 2016 at 9:14 AM, Peter Cock email@example.com wrote:
On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker firstname.lastname@example.org 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.
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. ...