error from VarScan

[shuang]

I was trying to run VarScan for variants calling. However, when I typed this command below,

$java net.sf.varscan.VarScan pileup2snp t01.pileup > outfile.snp


I received this error message below. What should I do?
PS. I've installed gcj-4.4-jre-headless on my computer.



Exception in thread "main" java.lang.NoClassDefFoundError: java
Caused by: java.lang.ClassNotFoundException: java
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
Could not find the main class: java. Program will exit.

[dkoboldt]

Hello,

It looks like you need to point Java to the VarScan Jar file, e.g.:

java -jar VarScan.jar pileup2snp t01.pileup > outfile.snp