This program is developed by Chunfeng Zheng, and refactored during Hackathon in Tucson in April 2014. A more detailed description of discrete steps of this pipeline is documented here.
##Compiling## The source files can be built using ant. The command below will compile the files into the build directory.
ant##Run the pipeline##
Please check the pipeline in run.sh.
./run.sh##Clean up## To remove the build directory run:
ant clean