Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support#285
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EddieLF wants to merge 5 commits into
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Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support#285EddieLF wants to merge 5 commits into
EddieLF wants to merge 5 commits into
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🐳 Expected TagsSome Dockerfiles have been modified in this PR. New tags are expected to be deployed.
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Similar to the latest Picard image which is now built from source using htsjdk 4.3.0 for compatibility with CRAM v3.1 #281, this PR is for building GATK from source for the same compatibility reasons.
Following the docs from the GATK repo:
r-base 4.3.1git lfsgatkrepo and then rungit lfs pull./gradlew ... -Dhtsjdk.version=4.3.0"gatk") with./gradlew localDevCondaEnvsource activate gatk