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Question: galaxy jobs with system-wide python
0
gravatar for tony.schreiner
2.3 years ago by
tony.schreiner • 20
tony.schreiner • 20 wrote:

Is it possible to run galaxy jobs with the system python instead of the virtualenv'ed one that runs the server?

I want to do that because of many packages available in the system python, that I don't want to install in the virtualenv; or for the time being, as tool dependencies.

Also open to hearing why this is a bad idea if it is.

Thanks
virtualenv python • 698 views
ADD COMMENT • link •
modified 2.3 years ago by Rob • 50 • written 2.3 years ago by tony.schreiner • 20

I expect it could be done with a wrapper shell script, but I'm hoping for a more direct way.

ADD REPLY • link written 2.3 years ago by tony.schreiner • 20
2
gravatar for tony.schreiner
2.3 years ago by
tony.schreiner • 20
tony.schreiner • 20 wrote:

Replying to myself here.

Not exactly an answer to my question, but my issue was solved by adding

import sys sys.path.append(...) sys.path.append(...)

for a few of the relevant original sys.path entries for the un-virtualized python.
ADD COMMENT • link written 2.3 years ago by tony.schreiner • 20

Thanks for taking the time to share back what worked!! Jen, Galaxy team

ADD REPLY • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for Rob
2.3 years ago by
Rob • 50
France
Rob • 50 wrote:

You can create your virtualenv with the --system-site-packages option. It will use all the system's libraries already installed on your system, and everything that you install in the future.
ADD COMMENT • link written 2.3 years ago by Rob • 50
0
gravatar for Hotz, Hans-Rudolf
2.3 years ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi Tony

I am still learning about virtualenv myself, but have you tried the following calls before calling the actual tool:

unset PYTHONPATH export PYTHONPATH=path_to_python_on_your_server

Hans-Rudolf
ADD COMMENT • link written 2.3 years ago by Hotz, Hans-Rudolf • 1.8k

after a deeper thought, this will most likely not work

sorry, Hans-Rudolf

ADD REPLY • link written 2.3 years ago by Hotz, Hans-Rudolf • 1.8k
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