Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support#285
Open
Build GATK from source with htsjdk 4.3.0 for CRAM v3.1 support#285
Conversation
🐳 Expected TagsSome Dockerfiles have been modified in this PR. New tags are expected to be deployed.
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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