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 <http://stackoverflow.com/questions/17709641/valueerror-numpy-dtype-has-th... 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(a)wur.nl