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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Follow up on CNN deprecation done in the update to python 3.10. #8907

Open samuelklee opened 4 months ago

samuelklee commented 4 months ago

After the updates to the python environment made in #8561, the CNN tools are no longer functional and were deprecated.

However, we may want to provide a separate environment in which some of these tools can still be used, perhaps in conjunction with NVScoreVariants. If so, we should also re-enable the relevant integration and WDL tests and provide appropriate documentation.

gokalpcelik commented 4 months ago

If we will get rid of those anyway can't we just provide a yml file with an unsupported yet minimal conda environment just to run old CNN tools (Neither we make it mandatory on the docker image nor we force people to install it). We should keep in mind that some of those libraries are pulled from the default channel which still raises questionable ethics for some.

droazen commented 4 months ago

Yes, the plan is to distribute the old environment as just a yml file that can be optionally activated -- provided that we can set up part of the test suite to run under the old environment, which is the next task.