For compiling Java code with MUSCLE, the Java archives in {{{$MUSCLE_HOME/share/muscle/java}}} and {{{$MUSCLE_HOME/share/muscle/java/thirdparty}}} should be added to the classpath. MUSCLE automatically includes these in the class path when running. To get these files formatted as a classpath, run
{{{
muscle2 --print-env=CLASSPATH
}}}

Modify the classpath of MUSCLE to add your own dependencies by adding the following lines to the configuration files
{{{
m = Muscle.LAST
m.add_classpath "path/to/dependency1.jar"
m.add_classpath "path/to/dependency2.jar"
}}}

The INCLUDE_PATH for C and C++ should include {{{$MUSCLE_HOME/include}}}, and the library path should include {{{$MUSCLE_HOME/lib}}}, specifically the {{{$MUSCLE_HOME/lib/libmuscle2.so}}} or {{{$MUSCLE_HOME/lib/libmuscle2.dylib}}} (depending on the operating system).