There are several ways to do this. The easiest is to use the uberjar release, which can be directly executed on any Java enabled platform. This makes it trivial to test and develop XPointer support in your applications, including server-side XPointer. The uberjar release contains a Java class org.CognitiveWeb.xpointer.XPointerDriver that provides a simple but flexible command line utility that exposes an XPointer processor. The XPointer is provided as a command line argument and the XML resource is read from stdin. The results are written on stdout by default as a set of null-terminated XML fragments. See XPointerDriver in the XPointer JavaDoc for more information.
If you already have a Java application, then it is straight-forward to integrate XPointer support using: org.CognitiveWeb.xpointer.XPointerProcessor You can see an example integration by looking at the XPointerDriver in the source code release.