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Mutect Build: Java requirements

noushin6noushin6 Baltimore, MDMember

Hello GATK team,

I am having a hard time trying to build mutect from the github repository, following the instructions at:

https://github.com/broadinstitute/mutect

Here are my questions:

1) What are the requirements for the java environment; i.e. does Mutect compile using OpenJDK or Sun JDK?

2) More specifically, I am getting the following error when running "mvn -Ddisable.queue install":

[ERROR] Failed to execute goal
com.pyx4j:maven-junction-plugin:1.0.3:link (link-public-testdata) on
project sting-aggregator: Can't create junction source
[/mnt/hn05_disk001/test/gatk-protected/public/gatk-framework/src/test/resources]
-> [/mnt/hn05_disk001/test/gatk-protected/public/testdata] -> [Help 1]

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