galaxy training - Calling variants in diploid systems gemini annotation source unavailable

usegalaxy.be support
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so i have been using the galaxy training for varinat calling and i am stuck at the gemini annotation step as there is no option to choose from in the gemini annotation source option

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Hi @varsha_sreekumar

It looks like the UseGalaxy.be server doesn’t host this reference index yet.

Two choices from here

  1. Use a much older version of the tool where the cached index is optional (the database isn’t required but expect to lose some context versus the tutorial).

  2. Try at a different UseGalaxy server for now instead.

Also, let’s ping the server administrators so they can learn about this. Hi @padge and @B0r1sD. This is the tutorial and any Gemini hg19 data is fine. There is one in the CVMFS resource. Ironically, the GTN tutorial is listing the BE server as the only one confirmed but I that is using tool versions, and ignores reference data. Be nice to get this running!

Thanks for reporting the problem and hopefully you are able to move forward with this! :slight_smile:

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Hey Varsha and Jennifer

That is annoying indeed. We will look into making the reference data available through CVMFS.

We will get back to you as soon as we have an update.

Kind regards
Boris from useGalaxy.be

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Hi @jennaj I don’t seem to find any loc files for gemini in either: /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml or /cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml. Would you be able to point me to where this reference data might be? browsing http://datacache.galaxyproject.org/ gives me 404 errors.

Edit: There does seem to be a data manager available for gemini, however I’m having trouble resolving the environment. I’ll try manually adding the reference data.

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Hi @padge I’m checking about the resource right now. And yes, the DM for this is complicated, and reference data is split between different tool versions. Loading up just the most current index should be “enough” as far as I know (that’s also what we host on ORG).

More soon.

Update: that was quick! Let us know if you can find it now!

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datacache.galaxyproject.org should be fixed now.

It looks like our only gemini databases on usegalaxy.org are locally installed and quite old.

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I managed to run the DM in a singularity container and the reference data shows up in the Data Tables however now the tool itself is running into several API errors, I’ll have to investigate further.

Eg:

galaxy.web.framework.decorators ERROR 2025-03-05 22:06:50,183 [pN:main.3,p:3166622,tN:WSGI_2] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/srv/galaxy/shared/src/lib/galaxy/web/framework/decorators.py", line 346, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "/srv/galaxy/shared/src/lib/galaxy/webapps/galaxy/api/tools.py", line 249, in build
    return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
  File "/srv/galaxy/shared/src/lib/galaxy/tools/__init__.py", line 2516, in to_json
    populate_state(request_context, self.inputs, params.__dict__, state_inputs, state_errors)
  File "/srv/galaxy/shared/src/lib/galaxy/tools/parameters/__init__.py", line 412, in populate_state
    _populate_state_legacy(
  File "/srv/galaxy/shared/src/lib/galaxy/tools/parameters/__init__.py", line 625, in _populate_state_legacy
    check_param(request_context, input, param_value, context, simple_errors=simple_errors)
  File "/srv/galaxy/shared/src/lib/galaxy/tools/parameters/__init__.py", line 246, in check_param
    value = param.from_json(value, trans, param_values)
  File "/srv/galaxy/shared/src/lib/galaxy/tools/parameters/basic.py", line 1072, in from_json
    if value in legal_values:
TypeError: unhashable type: 'dict'

edit:
It’s this error it seems: Uncaught exception in exposed API method: TypeError · Issue #19609 · galaxyproject/galaxy · GitHub

So the reference data should now be available for normal users

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Hi @padge

I wanted to make sure that you saw that the correction for the bug you noticed was merged into a release.

I’m not sure if the PR will backport or not, but asking at the development ticket could clarify more (saw your other comment, glad you found it!).

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Hi @jennaj Thanks for pointing this out. We’ve upgraded to 24.2 as of yesterday.

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