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  • how to install picard ?

    Hi there,

    I'm trying to use picard tools to remove duplicates from my sequence, but I'm having problem with installation. Has anyone installed picard-tools-1.57? Is there any detailed description about installing it in Unix? I downloaded and unzipped it, but don't know what to do for the next. I've never touched java before.

  • #2
    What problem are you having? Have you tried running one of the tools? What command are you using and what error are you getting?

    Comment


    • #3
      java -jar <INSERT THE JAR YOU WANT TO RUN HERE>
      should give you the help message for the given jar file.

      Comment


      • #4
        I tried to run MarkDuplicates.jar with the command

        java -jar ./picard-tools-1.57/MarkDuplicates.jar METRICS_FILE=rmdup.txt INPUT=$file.bam OUTPUT=$file.rmdup.bam REMOVE_DUPLICATES=true

        And got this error message

        Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:676)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:317)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:280)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:375)


        Originally posted by biznatch View Post
        What problem are you having? Have you tried running one of the tools? What command are you using and what error are you getting?

        Comment


        • #5
          What version of Java are you using? Picard requires 1.6.

          Comment

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