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. To get these files formatted as a classpath, run

muscle2 --print-env=CLASSPATH

MUSCLE automatically includes these in the class path when running. To add your own dependencies, modify the classpath of MUSCLE 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 executables should be linked with the $MUSCLE_HOME/lib/libmuscle2.so or $MUSCLE_HOME/lib/libmuscle2.dylib library (depending on the operating system). To add any other libraries to the dynamic library path, modify the configuration file as follows:

m = Muscle.LAST
m.add_libpath "path/to/dependency1/lib"
m.add_libpath "path/to/dependency2/lib"