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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Bump Galaxy ML version to 0.10.0 #1308

Closed anuprulez closed 1 year ago

anuprulez commented 1 year ago

ping @bgruening

bgruening commented 1 year ago

That needs some more work I think :(

anuprulez commented 1 year ago

Yes, started working on it. We may need to fix bugs in the Galaxy-ML python package.

anuprulez commented 1 year ago

After investigation, I found out that in the new Galaxy-ML version many python scripts as well as tools' XMLs have been updated. In addition, the method for saving models have also been changed that as a result changes the test data. Therefore, each ML tool needs to be investigated and updated accordingly and it may a take some time to finish all these tools. To begin, I have successfully updated the keras_model_builder tool and its tests pass locally.

keras_model_builder

I am saving all the changes here: https://github.com/anuprulez/galaxytools/tree/fix_galaxy_ml_1.0

anuprulez commented 1 year ago

Hi @kxk302 @paulzierep, I will need some help in upgrading Galaxy ML tools to the latest version (0.10.0). All tests of many tools should be updated and probably all the model files as the format of the saved model got changed from H5/Zip to H5MLM. I have done for several tools but still many are remaining.

The repo where I am stashing all the changes is: https://github.com/anuprulez/galaxytools/tree/fix_galaxy_ml_1.0

Here is the list of all tools for which tests are still failing:

Can you check and update the tests of these tools? Once these tests/tools are updated, we will need to adapt the training materials as well.

Let me know if you have questions!

Thanks a lot!

paulzierep commented 1 year ago

I will try to help as I can. Going through them step-by-step ...

kxk302 commented 1 year ago

Hi @anuprulez, I have a couple of deadlines and a bit busy, but will look next week.

anuprulez commented 1 year ago

Closing it in favour of https://github.com/bgruening/galaxytools/pull/1313