Needed (on your path): 
- Java SDK and JRE
- Cmake 2.8.0 (or higher)
- MinGW GCC compiler suite

Using eclipse:
Use ant on standalone.xml to build the molgenis.jar and setup the class files in the BUILD folder 

Add the following option to your .properties files
generate_cpp=true

Generate your project

Open a command shell and move to the generated/cpp folder

Check/Change the paths used in the CMakeList.txt to match your systems setup
Check/Change the paths used in the main.cpp to match your systems setup (char* classpath under the #includes)

CMake -G"MinGW Makefiles"
mingw32-make.exe clean
mingw32-make.exe

Now compilation will start after it is finished, run:

MolgenisCPP.exe

It will check mappings, and report any error then query the database for top level investigation objects