there is problem while installation the gatk tool .i have following things 1 download lastest version of gatk 3.7.0 2 java 1.8 3 installed tools BWA, SAMtools, Picard ,IGV ,RStudio IDE and R libraries ggplot2 and gsalib I extract files from gatk 3.7.0 and jar file is not executable during installation . kindly tell me how to install it on linux ubanto? i followed the command given in gatk tool installation document,but my problem not solved....
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fatimarasool135
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I have the same problem and I get this
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor version 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:800) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:449) at java.net.URLClassLoader.access$100(URLClassLoader.java:71) at java.net.URLClassLoader$1.run(URLClassLoader.java:361) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Which linux distribution do you have?
but I have already installed it and can't seem to replace the Java 7 version that the terminal always calls.
find the path to java 8 and use the full path to call gatk
/path/to/java_home/java -jar GenomeAnalysisTK.jar
or prepend the java_home to the path
export PATH=/path/to/java_home:${PATH}
java -jar GenomeAnalysisTK.jar
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Do you have a GenomeAnalysisTK.jar file? If yes, did you try
java -jar GenomeAnalysisTK.jar --help? If yes, what does it print to terminal?i typed command and get error unable to access jarfile genomeanalysistk.jar
Did you type
java -jar GenomeAnalysisTK.jar --helpin the directory where the GenomeAnalysisTK.jar is?Hello,
"But my problem not solved" is not a very useful description. Please tell us exactly what you have done.
There is no special procedure for installing gatk. Just download and unpack it. If java is correctly installed than you should use it like it is described in the documentation.
fin swimmer
i download setup..next how to unpack it?
Create a folder where you want to unpack gatk, e.g.:
Extract gatk to this folder:
Move into the folder:
Test if it works:
If you get any error messages please post it, so we can help more precisly.
fin swimmer