I don't like setting CLASSPATH. CLASSPATH is a global variable and as such it is evil:

• If you modify it in one script, suddenly some java programs will stop working.
• If you put there the libraries for all the things which you run, and it gets cluttered.
• You get conflicts if two different applications use different versions of the same library.
• There is no performance gain as libraries in the CLASSPATH are not shared - just their name is shared.
• If you put the dot (.) or any other relative path in the CLASSPATH that means a different thing in each place - that will cause confusion, for sure.

Therefore the preferred way is to set the classpath per each run of the jvm, for example:

Copyjava -Xmx500m -cp ".:../somejar.jar:../mysql-connector-java-5.1.6-bin.jar"    "folder.subfolder../dit1/some.xml

If it gets long the standard procedure is to wrap it in a bash or batch script to save typing.

I'm not a Java programmer, so I don't know the correct value for CLASSPATH. But, you seem to. You can add it to ~/.bashrc like so:

CLASSPATH=/path/to/1:/path/to/2:/etc

The change will take effect globally the next time you log in. However, it will take effect immediately in new shells.

Additionally, if you want to set it for just one particular command, do this:

CLASSPATH=/something command-here arg1 arg2

A third way would be to create a wrapper script, which would be appropriate if you needed to set multiple variables or if you needed to determine appropriate values programmatically:

#!/bin/bash
export CLASSPATH=/something
export ANOTHER_ENV_Variable=foo

exec your_fancy_program "$@"

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.