gatk tool installation problem

Question

[fatimarasool135]

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....

[grant.hovhannisyan]

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?

[fatimarasool135]

i typed command and get error unable to access jarfile genomeanalysistk.jar

[grant.hovhannisyan]

Did you type java -jar GenomeAnalysisTK.jar --help in the directory where the GenomeAnalysisTK.jar is?

[finswimmer]

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

[fatimarasool135]

i download setup..next how to unpack it?

[finswimmer]

Create a folder where you want to unpack gatk, e.g.:

mkdir gatk

Extract gatk to this folder:

tar -xvjf GenomeAnalysisTK.tar.bz2 -C gatk

Move into the folder:

cd gatk

Test if it works:

java -jar GenomeAnalysisTK.jar --version

If you get any error messages please post it, so we can help more precisly.

fin swimmer

Answer 1

[hdtms]

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)

[hdtms]

Also I read in the the GATK website that I need Java 1.8 to execute GATK, but I have already installed it and can't seem to replace the Java 7 version that the terminal always calls.

[finswimmer]

Which linux distribution do you have?

[Pierre Lindenbaum]

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