Question: galaxy jobs with system-wide python
0
gravatar for tony.schreiner
24 months ago by
tony.schreiner20 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 • 545 views
ADD COMMENTlink modified 23 months ago by Rob50 • written 24 months ago by tony.schreiner20

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

ADD REPLYlink written 23 months ago by tony.schreiner20
2
gravatar for tony.schreiner
23 months ago by
tony.schreiner20 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 COMMENTlink written 23 months ago by tony.schreiner20

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

ADD REPLYlink written 23 months ago by Jennifer Hillman Jackson25k
1
gravatar for Rob
23 months ago by
Rob50
France
Rob50 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 COMMENTlink written 23 months ago by Rob50
0
gravatar for Hotz, Hans-Rudolf
23 months ago by
Switzerland
Hotz, Hans-Rudolf1.8k 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 COMMENTlink written 23 months ago by Hotz, Hans-Rudolf1.8k

after a deeper thought, this will most likely not work

sorry, Hans-Rudolf

ADD REPLYlink written 23 months ago by Hotz, Hans-Rudolf1.8k
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