On Thu, Mar 3, 2016 at 3:24 AM, Linda Bakker <linda.bakker@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)

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

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:

Hi Linda,

There are two options here:

1. You can install your dependencies inside Galaxy's virtualenv, (by default, .venv)
2. You can set up a separate virtualenv to be used only by jobs. Depending on how you run jobs, this one may also need to include Galaxy's dependencies (to run the metadata detection step).

Details can be found here:


And specifically, the instructions for setting up a separate virtualenv for job handlers:



(.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?

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

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