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-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: [email protected]
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