WEPP/CMakeLists.txt at main · TurakhiaLab/WEPP · GitHub

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cmake_minimum_required (VERSION 3.8)
cmake_policy(SET CMP0069 NEW)
project(wepp)

if(NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE "RelWithDebInfo")
endif()

configure_file(src/version.hpp.in version.hpp)

set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -std=c++17 -Wall -Wno-unused-function  -Wno-deprecated-declarations")
set(CMAKE_CXX_FLAGS_DEBUG "-fsanitize=address -O0 -ggdb3 -fno-eliminate-unused-debug-symbols")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-DNDEBUG -O3")
set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3")
set(CMAKE_INCLUDE_CURRENT_DIR ON)

if(DEFINED ENV{CONDA_PREFIX} AND EXISTS "$ENV{CONDA_PREFIX}/include/google/protobuf/stubs/common.h")
    message(STATUS "Protobuf headers found in Conda. Using Conda paths.")
    set(Protobuf_INCLUDE_DIR "$ENV{CONDA_PREFIX}/include" CACHE PATH "" FORCE)
    if(APPLE)
        set(Protobuf_LIBRARY "$ENV{CONDA_PREFIX}/lib/libprotobuf.dylib" CACHE FILEPATH "" FORCE)
    else()
        set(Protobuf_LIBRARY "$ENV{CONDA_PREFIX}/lib/libprotobuf.so" CACHE FILEPATH "" FORCE)
    endif()
else()
    message(STATUS "Protobuf not found in Conda (or not using Conda). Using System paths.")
    unset(Protobuf_INCLUDE_DIR CACHE)
    unset(Protobuf_LIBRARY CACHE)
endif()

if(DEFINED Protobuf_PATH)
    find_package(Protobuf REQUIRED HINTS ${Protobuf_PATH})
else()
    find_package(Protobuf REQUIRED)
endif()

# Print version messages
if(Protobuf_FOUND)
    message(STATUS "Using Protocol Buffers ${Protobuf_VERSION}")
endif()
find_package(MPI REQUIRED)
include_directories(SYSTEM ${MPI_INCLUDE_PATH})
include_directories(${Protobuf_INCLUDE_DIRS})

find_package(TBB REQUIRED)

find_package(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED)

include_directories(${Boost_INCLUDE_DIRS})
file(GLOB WBE_SRCS "src/WEPP/*.cpp" "src/WEPP/*.hpp")

if(DEFINED Protobuf_PATH)
    protobuf_generate(
        LANGUAGE cpp
        TARGET wepp
        PROTOS sam.proto)

    protobuf_generate(
        LANGUAGE cpp
        TARGET wepp
        PROTOS parsimony.proto)

    add_executable(wepp
	    ${WBE_SRCS} ${PANMAT_SRCS}
    )

    add_executable(closest_peak_clustering
        src/closest_peak_clustering.cpp
    )
else()
    protobuf_generate_cpp(
        PROTO_SRCS PROTO_HDRS
        parsimony.proto)

    protobuf_generate_cpp(
        SAM_SRCS SAM_HDRS
        sam.proto)

    add_executable(wepp
	    ${WBE_SRCS}
        src/mutation_annotated_tree.cpp
        src/usher_mapper.cpp
        ${PROTO_SRCS} ${SAM_SRCS}
        ${PROTO_HDRS} ${SAM_HDRS}
        )

    add_executable(closest_peak_clustering
        src/closest_peak_clustering.cpp
    )
endif()

target_link_libraries(wepp PRIVATE stdc++ ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES})
target_link_libraries(closest_peak_clustering PRIVATE stdc++ TBB::tbb)