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!