You use either -jar or -cp, you can't combine the two. If you want to put additional JARs on the classpath then you should either put them in the main JAR's manifest and then use java -jar or you put the full classpath (including the main JAR and its dependencies) in -cp and name the main class explicitly on the command line

java -cp 'MyProgram.jar:libs/*' main.Main

(I'm using the dir/* syntax that tells the java command to add all .jar files from a particular directory to the classpath. Note that the * must be protected from expansion by the shell, which is why I've used single quotes.)

You mention that you're using Ant so for the alternative manifest approach, you can use ant's <manifestclasspath> task after copying the dependencies but before building the JAR.

<manifestclasspath property="myprogram.manifest.classpath" jarfile="MyProgram.jar">
  <classpath>
    <fileset dir="libs" includes="*.jar" />
  </classpath>
</manifestclasspath>

<jar destfile="MyProgram.jar" basedir="classes">
  <manifest>
    <attribute name="Main-Class" value="main.Main" />
    <attribute name="Class-Path" value="${myprogram.manifest.classpath}" />
  </manifest>
</jar>

With this in place, java -jar MyProgram.jar will work correctly, and will include all the libs JAR files on the classpath as well.

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.

Using Java 6 or later, the classpath option supports wildcards. Note the following:

• Use straight quotes (")
• Use *, not *.jar

Windows

java -cp "Test.jar;lib/*" my.package.MainClass

Unix

java -cp "Test.jar:lib/*" my.package.MainClass

This is similar to Windows, but uses : instead of ;. If you cannot use wildcards, bash allows the following syntax (where lib is the directory containing all the Java archive files):

java -cp "$(printf %s: lib/*.jar)"

(Note that using a classpath is incompatible with the -jar option. See also: Execute jar file with multiple classpath libraries from command prompt)

Understanding Wildcards

From the Classpath document:

Class path entries can contain the basename wildcard character *, which is considered equivalent to specifying a list of all the files in the directory with the extension .jar or .JAR. For example, the class path entry foo/* specifies all JAR files in the directory named foo. A classpath entry consisting simply of * expands to a list of all the jar files in the current directory.

A class path entry that contains * will not match class files. To match both classes and JAR files in a single directory foo, use either foo;foo/* or foo/*;foo. The order chosen determines whether the classes and resources in foo are loaded before JAR files in foo, or vice versa.

Subdirectories are not searched recursively. For example, foo/* looks for JAR files only in foo, not in foo/bar, foo/baz, etc.

The order in which the JAR files in a directory are enumerated in the expanded class path is not specified and may vary from platform to platform and even from moment to moment on the same machine. A well-constructed application should not depend upon any particular order. If a specific order is required then the JAR files can be enumerated explicitly in the class path.

Expansion of wildcards is done early, prior to the invocation of a program's main method, rather than late, during the class-loading process itself. Each element of the input class path containing a wildcard is replaced by the (possibly empty) sequence of elements generated by enumerating the JAR files in the named directory. For example, if the directory foo contains a.jar, b.jar, and c.jar, then the class path foo/* is expanded into foo/a.jar;foo/b.jar;foo/c.jar, and that string would be the value of the system property java.class.path.

The CLASSPATH environment variable is not treated any differently from the -classpath (or -cp) command-line option. That is, wildcards are honored in all these cases. However, class path wildcards are not honored in the Class-Path jar-manifest header.

Note: due to a known bug in java 8, the windows examples must use a backslash preceding entries with a trailing asterisk: https://bugs.openjdk.java.net/browse/JDK-8131329

The ClassPath environment variable is only used when you want your computer to look at a specific location for your .class files; generally speaking, it doesn't exist unless you make it exist, whether on purpose or a side effect of some installer.

Most of the time, the applications you are running (primarily JRE), know exactly where to look for .class files. Most of the time.

However, if you were refering to the PATH environmental variable, that can be more of an issue.

Oracle has a throughout step-by-step on setting your enviromental variables (I can vouch, I just had to reset my PATH this morning): http://docs.oracle.com/javase/tutorial/essential/environment/paths.html

However, here are the steps as I remember them:

1. Start Menu, right click Computer, Choose Properties
2. Advanced System on the far left, and there is an Enviromental Variables button near the bottom, click it
3. In the bottom context menu, find the PATH variable and choose edit
4. Put a semicolon after the last one, and then add "C:\Program Files\Java\jre7\lib;" and "C:\Program Files\Java\jre7\bin;" or wherever your java "lib" and "bin" folders are

And then you should be all swell and dandy, no harm no fowl.