The problem with using Java on Cygwin is that Java.exe is a windows program and expects the path to be in windows style. Whereas Cygwin expects paths to be in Unix style.
Hence if U run a simple Java command like the below, U will get an error:
java -classpath /cygdrive/d/naren MyJavaProgram
Even the following would give an error, bcoz cygwin cannot understand windows path on the command prompt
java -classpath d:\naren MyJavaProgram
So, the solution is to use a cygwin utility known as cygpath.exe. This tool converts from unix paths to windows path, before passing it to the shell.
java -classpath `cygpath -wp $CLASSPATH` [arguments]