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Old 12-14-2011, 04:27 PM   #1
eilosei
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Question 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.
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Old 12-14-2011, 05:53 PM   #2
biznatch
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What problem are you having? Have you tried running one of the tools? What command are you using and what error are you getting?
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Old 12-14-2011, 05:54 PM   #3
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Quote:
java -jar <INSERT THE JAR YOU WANT TO RUN HERE>
should give you the help message for the given jar file.
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Old 12-14-2011, 08:27 PM   #4
eilosei
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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)


Quote:
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?
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Old 12-15-2011, 07:17 AM   #5
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What version of Java are you using? Picard requires 1.6.
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