CMakeLists.txt

cmake_minimum_required(VERSION 3.7)

include(ExternalProject)

#set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
#add_compile_options(-Werror)

list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)

# set the project name
project(chips VERSION 2.4)
configure_file(chipsConfig.h.in chipsConfig.h)

# specify the C++ standard
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)

ExternalProject_Add(zlib
        PREFIX ${CMAKE_BINARY_DIR}/thirdparty/zlib
        GIT_REPOSITORY "https://github.com/madler/zlib.git"
        GIT_TAG "v1.2.8"
        UPDATE_COMMAND ""
        BUILD_IN_SOURCE 1
        CONFIGURE_COMMAND ${CMAKE_BINARY_DIR}/thirdparty/zlib/src/zlib/configure --prefix=${CMAKE_BINARY_DIR}/thirdparty/zlib --static
        INSTALL_DIR ${CMAKE_BINARY_DIR}/thirdparty/zlib
        LOG_DOWNLOAD 1
        LOG_INSTALL 1
        )
ExternalProject_Add(htslib
        PREFIX ${CMAKE_BINARY_DIR}/thirdparty/htslib
        GIT_REPOSITORY "https://github.com/samtools/htslib.git"
        GIT_TAG "1.3.1"
        UPDATE_COMMAND ""
        BUILD_IN_SOURCE 1
        CONFIGURE_COMMAND ""
        BUILD_COMMAND make
        INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/thirdparty/htslib
        LOG_DOWNLOAD 1
        )

include_directories(${CMAKE_CURRENT_SOURCE_DIR})
include_directories(${CMAKE_BINARY_DIR}/thirdparty/zlib/include)
set(zlib_static ${CMAKE_BINARY_DIR}/thirdparty/zlib/lib/libz.a)
set(htslib_static ${CMAKE_BINARY_DIR}/thirdparty/htslib/lib/libhts.a)
include_directories(${CMAKE_BINARY_DIR}/thirdparty/htslib/include)
add_dependencies(htslib zlib)

add_subdirectory(lib)

# add the executable
add_executable(chips src/main.cpp)

target_compile_features(chips PRIVATE cxx_range_for)
target_include_directories(chips PUBLIC "${PROJECT_BINARY_DIR}")
target_link_libraries(chips ChIPs pthread)
install(TARGETS chips DESTINATION bin)

add_dependencies(htslib zlib)
add_dependencies(ChIPs htslib)

set(CPACK_DEBIAN_PACKAGE_MAINTAINER "") #required

set(CPACK_PACKAGE_VERSION "${chips_VERSION_MAJOR}.${chips_VERSION_MINOR}")
set(CPACK_PACKAGE_VERSION_MAJOR "${chips_VERSION_MAJOR}")
set(CPACK_PACKAGE_VERSION_MINOR "${chips_VERSION_MINOR}")

set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/README.md")

set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_SOURCE_DIR}/build/;${CMAKE_SOURCE_DIR}/.git/;${CMAKE_SOURCE_DIR}/power-analysis/;${CMAKE_SOURCE_DIR}/paper-analyses/;${CMAKE_SOURCE_DIR}/paper-methods/")

include(CPack)