Add data manager for clair3 models #6659
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| <requirement type="package" version="3.12">python</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><
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What is the known_models code doing?
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It ensures that the same model is not downloaded twice (duplicates are not allowed in the data table).
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| <tables> | |||
| <table name="clair3_models" comment_char="#" allow_duplicate_entries="False"> | |||
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I would have assumed that Galaxy automatically does not allow duplicates if allow_duplicate_entries="False".
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Alternatively the value_in_data_table might be easier?
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Nope, it lets you provide duplicate entries and then gives an error.
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value_in_data_table works for manually entered values, but doesn't work for the latest mode - i.e. where the DM downloads the latest models.
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In a discussion with Jack Jacobs of ONT this morning he confirmed that ONT would prefer some kind of wording associated with a checkbox that users can check to acknowledge that they comply with the terms of ONT's license for these models. He will revert with specific wording. The main concern from ONT is not a commercial user simply using the models but rather a commercial user using the models to compete with ONT - that said, I will wait on the wording. He also recommended a direct model download tool that can download the .tar.gz version of the models to the user history to ensure that they have the latest version of the models. This will be a separate project. Finally he confirmed that the model name uniquely identifies a model: i.e. there will not be "silent updates" of models. In conclusion, from this discussion I think:
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Not sure. Why? |
Well, yes, lets wait for that, but as long as the model is supplied via a data manager any user, commercial or not, will not have direct access to it. |
As noted in #6547 the clair3 tool does not come with models for newer Oxford Nanopore flow cells (the R10 flow cells). These are provided by Oxford Nanopore on their Rerio page. This data manager fetches Clair3 models from that page.
NOTE: While this tool has no restrictions, the license on the Rerio page ("Oxford Nanopore Technologies, Ltd. Public License Version 1.0") is difficult to interpret and might not permit the use of the downloaded models in a commercial context. This is similar to 'research use only' tools like the BRAKER3 one (https://github.com/genouest/galaxy-tools/tree/master/tools/braker) and IUC folks need to decide on whether to include this DM in the repository, thus I have not checked the "License permits unrestricted use (educational + commercial)" box for now.
FOR CONTRIBUTOR: