I broke my Galaxy server by setting LC_ALL="en_US.UTF-8"

1

Hi all,

I’m admin of a Galaxy installation that I inherited but I don’t know much about it yet. We have a lot of tools installed and a lot of users using the tools.

I was troubleshooting one tool that didn’t run properly, it threw an error on some unicode character that it couldn’t parse as ascii text. In my troubleshooting I modified the /path/to/galaxy/.venv/bin/activate that Galaxy runs in to include:

export LC_ALL=“en_US.UTF-8”

To run Galaxy with unicode so this tool might work. Previously LC_ALL was not set.
After I restarted Galaxy, none of the tools run, they all remain in a gray state with the message:

This is a new dataset and not all of its data are available yet.
format fasta.gz database [?]

Not sure what is going on, but since my change seems to have broken stuff I have reverted my change and restarted Galaxy again. I have verified that the venv doesn’t have LC_ALL set (when I source it myself and run os.environ). However, Galaxy is still broken. None of my test jobs start, they are stuck on the same message:

“This is a new dataset and not all of its data are available yet.”

What could be going on?

2

I cannot give a solution but I think someone that is able to give a solution needs more info.

What version of galaxy are you using?
How do you start/stop galaxy?
And did you check the log files already?

Keep in mind galaxy is sort of a wrapper around the tools. If a tool gives a specific error you need to check the code of the tool, not of galaxy.

Don’t try it now but you could let galaxy recreate the virtualenv if needed.

I cannot think of any reason to modify a file like “/path/to/galaxy/.venv/bin/activate”, but for future use if you ever need to you can use virtualenvwrapper for this:

1 Like
3

Thanks @gbbio!

I thought I broke it with this change but it turned out it was someone else’s change. I tracked that one down and reverted it and Galaxy is fine again. (The change had to do with slurm-drmaa).

You’re right that I should troubleshoot the tool and not the Galaxy instance. Either way my attempt to include LC_ALL didn’t even fix my issue after I found and resolved the reason jobs weren’t starting…

I have more homework to do. Thanks for your help!