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[DO NOT MERGE]#9045

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jamesemery wants to merge 37 commits intomasterbroadinstitute/gatk:masterfrom je_updateCondaEnvironmentbroadinstitute/gatk:je_updateCondaEnvironmentCopy head branch name to clipboard

+11,164-3

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Commits on Nov 12, 2024

• first attempt at a changed environment

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Commits on Nov 15, 2024

• updating pytorch to newer version that carries some risk

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• gore

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• back to basics

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• uncommenting some

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• trying two more dependencies

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• enabling two more

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Commits on Nov 18, 2024

• was it cyvcf?

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• mmninga?

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Commits on Nov 19, 2024

• another minor alteration of python environment

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• bioconda cyvcf2 is probably a conflict

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• bioconda cyvcf2 is probably a conflict

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Commits on Dec 4, 2024

• Reverting to 2.1.0

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Commits on Dec 9, 2024

• trying to bundle the cuda installation via conda

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• pairing up the correct cuda compatable pytroch version

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• change the channel

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• testing with only cuda backend?

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• change the channel

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Commits on Dec 10, 2024

• testing if the other mkl invocation was the problem

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• testing if the other mkl invocation was the problem

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• finally! python has lead us from gods light

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• finally! python has lead us from gods light

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• this should probably work

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Commits on Dec 19, 2024

• put the code in the right place, now need to build a pythonscriptexecutor to run it and make sure it gets installed for running correctly

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Commits on Jan 10, 2025

• hopefully what is needed for docker building proper

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• did this really stop working?

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• python installation is dizzying

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• moving the cuda drivers into the right stage of the build

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Commits on Jan 13, 2025

• names have power

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• fixing a silly mistake

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Commits on Jan 15, 2025

• made a somewhat robust mechanism for converting to the python argument outputs for permutect

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Commits on Jan 16, 2025

• some more script editing

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• some more script editing

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Commits on Jan 17, 2025

• added the next few tasks from the main wdl

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• added the next few tasks from the main wdl

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Commits on Jan 21, 2025

• added docstore bindings to the permutect wdls

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• maybe the branches are the problem

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