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)

source my_galaxy_dir/.venv/bin/activate
pip install scipy (dependency numpy also installed)
./run.sh

But since the last update, i am having problems with this.
Did something change? because it looks like it searches for an existing venv and then activates a new venv in my already active one??

Depending on what i try, when i execute my tool in galaxy, my messages range from

ImportError: No module named scipy
or ValueError: numpy.dtype has the wrong size, try recompiling

I tried running galaxy without a venv, re-creating my venv. renaming my venv
installing numpy, then scipy, not using pip at all.
removing numpy and reinstalling without cache.
I also played around with pip, doing nothing after creating my venv, or first upgrading my pip, but then after i start galaxy i get this message:

(.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...can someone tell me the correct way to start galalxy within or without my venv and how to correctly install my packages?
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