how to install picard ?

[eilosei]

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.

[biznatch]

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

[nilshomer]

java -jar <INSERT THE JAR YOU WANT TO RUN HERE>

should give you the help message for the given jar file.

[eilosei]

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)

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

[biznatch]

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