CMakeLists.txt example

cmake_minimum_required(VERSION 2.6)
project(bayesembler)

set(CMAKE_CXX_COMPILER "g++")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")

set(BOOST_LIB_DIR <PATH_TO_BOOST_LIB_DIR>)
set(BOOST_INCLUDE_DIR <PATH_TO_BOOST_INCLUDE_DIR>)
set(BAMTOOLS_LIB_DIR <PATH_TO_BAMTOOLS_LIB_DIR>)
set(BAMTOOLS_INCLUDE_DIR <PATH_TO_BAMTOOLS_LIB_DIR>)
set(EIGEN_INCLUDE_DIR <PATH_TO_EIGEN_INCLUDE_DIR>)

include_directories(. ${BOOST_INCLUDE_DIR} ${BAMTOOLS_INCLUDE_DIR} ${EIGEN_INCLUDE_DIR})
link_directories(${BOOST_LIB_DIR} ${BAMTOOLS_LIB_DIR})

add_executable(${PROJECT_NAME} main.cpp gibbsSampler.cpp alignmentParser.cpp allPaths.cpp gammaGenerator.cpp simplexSizeGenerator.cpp expressionGenerator.cpp assignmentGenerator.cpp valueContainer.cpp sequencingModel.cpp gibbsOutput.cpp assembler.cpp fragmentLengthModel.cpp)

target_link_libraries(${PROJECT_NAME} boost_math_c99 bamtools boost_program_options boost_regex boost_graph boost_thread boost_system boost_filesystem)