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Unable to access jarfile /GenomeAnalysisTK.jar

First of all, did not find exact name "Java 1.8.x" on the Ubuntu Software Center. I had to search the web to finally get a program called Java Platform (JDK). Would be good to give some more info on how to get that certain Java and if JDK works or not on the quickstart page (https://software.broadinstitute.org/gatk/documentation/quickstart).

After downloading JDK and ckecking the java version I get "openjdk version 1.8.0.91".

After typing the command java -jar /path/to/GenomeAnalysisTK.jar -h i get the answer "Unable to access jarfile /GenomeAnalysisTK,jar"

Did i download the wrong Java? If so, where can I find the right one for this case.

Answers

  • You have to put in the actual path to the GenomeAnalysisTK.jar file, which I guess isn't "/GenomeAnalysisTK.jar" on your system.

    Please also copy/paste the exact command and error messages you get, don't type them over or you'll make errors that make it hard to help you. Like this:

    $ java -jar /path/to/GenomeAnalysisTK.jar -h
    Error: Unable to access jarfile /path/to/GenomeAnalysisTK.jar

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