Gemini database installation crash

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1

Hi,

I am running Galaxy 24.1 on Ubuntu 24.04 and the installation of Gemini seems problematic. I installed the latest available version and the data manger for Gemini. I downloaded the database with the datamanger (after fixing here libzlib bugs for the automatic conda environment creation) and now all tools which require the database of Gemini, ‘Gemini load’, ‘Gemini fusions’, ‘Gemini interactions’ and ‘Gemini pathways’ crash with

Loading tool toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2 failed: Error: Uncaught exception in exposed API method:

Looking in galaxy.log the error is:

galaxy.web.framework.decorators ERROR 2025-03-13 10:04:24,444 [pN:main.1,p:1325358,tN:WSGI_0] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/home/galaxy/galaxy/lib/galaxy/web/framework/decorators.py", line 346, in decorator
    rval = func(self, trans, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/api/tools.py", line 249, in build
    return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 2510, in to_json
    populate_state(request_context, self.inputs, params.__dict__, state_inputs, state_errors)
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/__init__.py", line 412, in populate_state
    _populate_state_legacy(
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/__init__.py", line 525, in _populate_state_legacy
    state[input.name] = input.get_initial_value(request_context, context)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line 1118, in get_initial_value
    options = list(self.get_options(trans, other_values))
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line 970, in get_options
    return self.options.get_options(trans, other_values)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/dynamic_options.py", line 888, in get_options
    options = self.get_fields(trans, other_values)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/dynamic_options.py", line 764, in get_fields
    options = filter.filter_options(options, trans, other_values)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/galaxy/galaxy/lib/galaxy/tools/parameters/dynamic_options.py", line 537, in filter_options
    return sorted(options, key=lambda x: x[self.column], reverse=self.reverse)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: '<' not supported between instances of 'dict' and 'str'

Googling this error message it seems to me a Python 2 vs Python 3 issue. Not sure if this really applies here, given that to load the database seems to work on usegalaxy.org and usegalaxy.eu.

Maybe someone has an idea what the issue is?

Thanks a lot!

2

Welcome @casio

Thanks for posting all of the details!

I think the problem you are having is similar to what others have noticed about this DM. I’ve asked at the Admin chat since I am not sure what the correction is exactly. It is probably with the environment, but I also know some were just loading the data directly without the DM.

This is the chat link. They will probably reply here but feel free to join the chat too! :slight_smile: You're invited to talk on Matrix

3

This is the most current topic. Maybe it is not resolved. → galaxy training - Calling variants in diploid systems gemini annotation source unavailable - #7 by padge

Hi @padge – were you able to solve this? If yes, would you have time to post back what you needed to do? Thank you!

4

@casio Can you try upgrading Galaxy to 24.2.2?

This issue should have been solved by: Uncaught exception in exposed API method: TypeError · Issue #19609 · galaxyproject/galaxy · GitHub

1 Like
5

Great, thank you @nuwang !!

6

I had to run the DM inside a singularity container for it to work. In the mean time we’ve also upgraded to 24.2 however.

1 Like
7

Thanks for the tip with upgrading to 24.2.3, that helped. Now I have new bugs, but will open a new issue for this.