New data manager for clair3 models

usegalaxy.org support
,
1

The clair3 variant caller for ONT long read data makes use of models tuned for different ONT chemistries, flow cells, etc. A new data manager data_manager_clair3_models has recently been added to tools-iuc, which downloads models from the Oxford Nanopore rerio repository - these are needed for the ONT R10 flow cells. Updates have also been made to the clair3 and artic tools, letting them use these new models.

The new models from the rerio repository are not under an open license, so the new versions of the clair3 and artic tools include a checkbox (used only when using rerio models) to force people to acknowledge their compliance with the license between using the tools.

Please install the new DM on usegalaxy.org, run it to download the latest ONT Rerio models and upgrade the clair3 and artic tools.

Thanks,
Peter

2

Hi @Peter_van_Heusden Hope you are doing well!

For the indexing part, a ticket against the IDC to have these new references added to the CVMFS mount is the path for the data addition. Then the tool install/update is a separate request.

I’ve created the tickets here to get that started. This is for all UseGalaxy, yes? It looks like the tools didn’t get a version bump so I wasn’t quite sure if the tools themselves are updated on the servers but I’m guessing not at least at ORG and AU since I don’t see the license agreement checkbox (but I do see that at EU).

Would you help to clarify what I missed on those tickets? Thanks! :slight_smile: