Question: gatk tool installation problem
0
gravatar for fatimarasool135
14 months ago by
fatimarasool1350 wrote:

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....

snp R software error • 1.3k views
ADD COMMENTlink modified 12 months ago by hdtms 20 • written 14 months ago by fatimarasool1350
3

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?

ADD REPLYlink written 14 months ago by grant.hovhannisyan1.1k

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

ADD REPLYlink written 14 months ago by fatimarasool1350

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

ADD REPLYlink written 14 months ago by grant.hovhannisyan1.1k
1

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

ADD REPLYlink written 14 months ago by finswimmer5.4k

i download setup..next how to unpack it?

ADD REPLYlink written 14 months ago by fatimarasool1350

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

ADD REPLYlink modified 14 months ago • written 14 months ago by finswimmer5.4k
0
gravatar for hdtms
12 months ago by
hdtms 20
hdtms 20 wrote:

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)

ADD COMMENTlink written 12 months ago by hdtms 20
1

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.

ADD REPLYlink written 12 months ago by hdtms 20

Which linux distribution do you have?

ADD REPLYlink written 12 months ago by finswimmer5.4k

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
ADD REPLYlink written 12 months ago by Pierre Lindenbaum112k
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