Setting an environment variable for python tools

Hello everyone,

I have some python scripts that are contacting an external server in order to produce their results.

I would like to pass the IP of that external server as an environment variable in the python scripts.

Right now the python tools do not see the variables even if it is set in the /etc/environment. I also tried setting the variables in the galaxy service.

Any ideas how I can pass the variables inside the python tools?

Thanks a lot,
Thanasis.

I have discovered the environment_setup_file option in the galaxy.ini file. Is there documentation anywhere on how it works?

I was thinking to setup the environment using that option because as it says here:
https://galaxyproject.org/admin/config/tool-dependencies/#galaxy-specific-environment-file
it is being run before the tools.

So, any more documentation anywhere?

1 Like

Try here: https://docs.galaxyproject.org/en/master/index.html

I’ll also ping for more pro admin help on Monday. Apologies for delayed reply!