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Update the GATK base image to a newer LTS ubuntu release #8610

Merged
merged 13 commits into from
Dec 12, 2023
Merged

Update the GATK base image to a newer LTS ubuntu release #8610

merged 13 commits into from
Dec 12, 2023

Commits on Dec 8, 2023

  1. Update the GATK base image to a newer LTS ubuntu release

    @droazen
    droazen committed Dec 8, 2023
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Commits on Dec 9, 2023

  1. Incorporate base image changes from Sam Lee's PR, fix md5 check, othe… 

    …r changes
    @droazen
    droazen committed Dec 9, 2023
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  2. pip

    @droazen
    droazen committed Dec 9, 2023
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  3. Back out update to newer conda, try 20.04 instead of 22.04

    @droazen
    droazen committed Dec 9, 2023
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  4. Back to 22.04

    @droazen
    droazen committed Dec 9, 2023
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Commits on Dec 10, 2023

  1. Add an h5diff epsilon + reporting of differences to ScoreVariantAnnot… 

    …ationsIntegrationTest and TrainVariantAnnotationsModelIntegrationTest
    @droazen
    droazen committed Dec 10, 2023
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Commits on Dec 11, 2023

  1. Capture h5diff output in exception messages

    @droazen
    droazen committed Dec 11, 2023
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  2. Remove epsilon temporarily

    @droazen
    droazen committed Dec 11, 2023
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  3. restore epsilon, add debugging statement

    @droazen
    droazen committed Dec 11, 2023
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  4. Remove debugging, remove obsolete runSystemCommand() method, final re… 

    …factoring
    @droazen
    droazen committed Dec 11, 2023
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  5. Incorporate Sam L patch to upgrade conda + pip

    @droazen
    droazen committed Dec 11, 2023
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  6. One more test with epsilon off to make sure reporting is still working

    @droazen
    droazen committed Dec 11, 2023
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  7. Restore epsilon, switch to release base image, update scripts and docs

    @droazen
    droazen committed Dec 11, 2023
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