Say you have multiple jar files a.jar,b.jar and c.jar. To add them to classpath while compiling you need to do

$javac -cp .:a.jar:b.jar:c.jar HelloWorld.java

To run do

$java -cp .:a.jar:b.jar:c.jar HelloWorld

CLASSPATH is not meant to search for jars. It is meant to search for classes. Putting a jar in CLASSPATH means java will see the classes inside the jar, but not the jar itself.

What you want is more likely a shell script wrapper starting the jar.

Create a text file containing the following lines:

#!/bin/sh
java -jar /usr/local/bin/gatk/GenomeAnalysisTK.jar

Make the file executable (suppose you name it GenomeAnalysisTK):

chmod +x GenomeAnalysisTK

Put that file in /usr/local/bin or ~/bin or wherever you want provided the path is in your $PATH.

From now on you can call the shell script and it will start the jar. No need to mess with CLASSPATH anymore.

Alternatively: with the jar in the classpath you can start the main class from inside the jar like this:

java org.broadinstitute.sting.gatk.CommandLineGATK

The main class of the jar is specified in the file META-INF/MANIFEST.MF inside the jar. For more information see the wikipedia article about jar files.

First thing to note - you're not using "Putty" to set the CLASSPATH, you're using the 'shell' that you login to, using Putty as your SSH client.

Depending on your shell, there are different ways to set your classpath -

Bash (or compatible shells

export CLASSPATH=/full/path/to/xalan.jar:/full/path/to/serializer.jar:/full/path/to/xml-apis.jar:/full/path/to/xercesImpl.jar:$CLASSPATH

C Shell (or compatible shells)

setenv CLASSPATH /full/path/to/xalan.jar:/full/path/to/serializer.jar:/full/path/to/xml-apis.jar:/full/path/to/xercesImpl.jar:$CLASSPATH

For JAR files, you have to set the CLASSPATH and not the PATH environment variable.

If you're using BASH, it is: export CLASSPATH="$CLASSPATH:<full_path_to_each_jar_files>"

You better add it in the file .bashrc unless you know what you are doing.

Example:

export CLASSPATH="$CLASSPATH:$HOME/java/lib/foebar.jar:$HOME/extra/lib/another.jar"

But of course, if you are still invoking the jar file with the Main class you have to use the full path for it:

java -jar $HOME/java/lib/main-prog.jar

However, you can set its execution right and run it:

chmod u+x $HOME/java/lib/main-prog.jar
export PATH=$PATH:$HOME/java/lib
main-prog.jar

But you have to take care that your classpath is correct and list all required jar.

OK, I finally figured this out by myself. This is how you correctly add modules, which the JAR expects to be present:

/usr/bin/java --module-path /usr/share/java/jaxws-api.jar --add-modules jaxws.api -jar exchange-sync.jar

So it does not really have anything to do with the classpath, it's just about adding the module.

To set the classpath, it is in most cases better to use the the -cp or -classpath argument when calling javac and java. It gives you more flexibility to use different classpaths for different java applications.

With the -cp and -classpath arguments your classpath can contain multiple jars and multiple locations separated with a : (colon)

javac -cp ".:/somewhere/A.jar:/elsewhere/B.jar" MyClass.java
java -cp ".:/somewhere/A.jar:/elsewhere/B.jar" MyClass

The classpath entry in the example sets the classpath to contain the current working directory (.), and the two jar files A.jar and B.jar.

If you want to use the CLASSPATH environment variable you can do

export CLASSPATH=".:/somewhere/A.jar:/elsewhere/B.jar"
javac MyClass.java
java MyClass

Try this

java -classpath ./db2jcc_license_cu.jar:./db2jcc4.jar:. CreateCoffees

when you use -classpath it looses current directory from classpath so it needs . in classpath as well explicitly