GATK4 from conda-forge not working with java version 11

bioconda / bioconda-recipes

Conda recipes for the bioconda channel.

https://bioconda.github.io

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GATK4 from conda-forge not working with java version 11 #35268

Open SusiJo opened 2 years ago

SusiJo commented 2 years ago

Hi, I hope I'm not missing something essential - but when running gatk4 Markduplicatesspark with a conda environment using bioconda::gatk4=4.2.3.0 (also when using the latest version) I get a USER ERROR Caused by:Unsupported class file major version 55. This sound like a problem with the java version and I was wondering if the right version could be set in the bioconda recipe. If that is related to another problem though, I'd appreciate any help.

Cheers

SusiJo commented 2 years ago

Update: I was able to get Markduplicatesspark to run, but only when explicitly installing Openjdk 1.8 alongside with it (bioconda::gatk4=4.2.3.0 conda-forge::openjdk=8.0.312). When creating an environment with just gatk4, Openjdk version 11.0.9.1 is installed which seems to be incompatible with gatk4. Could you please fix this in the recipe?