My local Galaxy can longer read my datatable.loc files

[jean.le-cras]

Hello,

I’m developing tools that read datatable.loc files from the tool-data folder. My tools were able to read this data successfully until I restarted my local instance and got the error galaxy.tool_util.data WARNING 2026-02-27 10:19:24,124 [pN:main,p:34614,tN:MainThread] Line 2 in tool data table ‘countries’ is invalid (HINT: ‘’ characters must be used to separate fields):
ABW Aruba (Neth.) {‘xmin’: -70.0638427734375, ‘ymin’: 12.411824226379395, ‘xmax’: -69.86544799804688, ‘ymax’: 12.623372077941895}’ characters must be used to separate fields) for each line of the data table (‘<TAB>’ without markdown). Before restarting the instance, it was working fine, and I haven’t modified the files since. I checked that the columns are separated by tabs.

I modified the tool_conf.xml.sample file, but I don’t see how that could be the reason. A colleague suggested that it might be due to a Galaxy update, but I didn’t do a git pull. The commit tag for my Galaxy instance is v24.1-7482-g8a19c8a8fe.

[jennaj]

Hi @jean.le-cras

Thanks for sharing these details! It sounds like you didn’t run an update (or didn’t intend to!).

Some questions. If I had to guess, there is something different about what the job runtime environment “sees” after the restart. So, not the Galaxy database/data itself, but instead what the tool wrapper has access to at runtime. Probably some package you are calling in the script. (If this turns out to be it, you could trap missing dependencies, or harden the required versions, or create a stable job container.). But this is all just a guess! Let’s see what you have!

0. Any other concurrent updates? OS? Dependencies like Python or packages called out by the wrapper?

1. What command string did you use for the restart?

2. Have you check to make sure that all services (remote directories or environments or clusters) are still connected to your server?

3. What does the job environment look like? Did the before and after jobs run in different environments? A container? Comparing what was actually used between runs will provide some clues.

4. Finally, are you using Planemo for your tool development? If not, it can also help with troubleshooting.

@jennaj

Are you using Planemo for your development project yet? If not, I would start there, then see what it reports. The framework will help with all steps to get your wrapper published later on, too.

@jennaj

Planemo

Planemo can help with container packaging, tool testing, and practical items such as building up the xml tool form that end users will interact with.

• https://planemo.readthedocs.io/ << please see the Quick Start guide for more general context

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Let’s start there! Please let us know if you solve this before we dig in here!

[jean.le-cras]

Thank you for your reply.

I didn’t update Galaxy manually, I was wondering if it did it automatically.

I solved the problem, I’m not sure how I did it, but I did a git stash and a git pull and deleted the first line of data, now it works again.

[jennaj]

I’m glad your update worked! Thanks for letting us know