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GATK Queue support » History » Version 1

Brett Smith, 01/12/2016 06:24 PM

1 1 Brett Smith 
h1. GATK Queue support
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We have code that integrates GATK Queue with Arvados, creating child jobs for each work unit spawned by GATK Queue.  "Source is on GitHub":https://github.com/curoverse/gatk-protected





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Build process:





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# Install Maven, dependencies, and plug-ins: @sudo aptitude install openjdk-7-jdk maven libmaven-jar-plugin-java libmaven-shared-jar-java libmaven-compiler-plugin-java@





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# Build and install the Arvados Java SDK.  In @arvados/sdk/java@, run: @mvn package -Dmaven.test.skip=true && mvn install -Dmaven.test.skip=true@





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# Build GATK Queue.  In @gatk-protected@, run: @mvn package@





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If it succeeds, you'll have @target/Queue.jar@.  Our GATK Queue jobs to date run that jar from a collection, so @arv keep put@ it where you need it.