/
CMakeLists.txt
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CMakeLists.txt
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# Still needs
## [ ] Build & Release options
## [ ] Build with debug option
## [ ] Build test cases option
## [ ] Build and generate static library option
## change the static linking options to something cmake
# Minimum cmake version
cmake_minimum_required (VERSION 3.14...3.20)
# Name of project and that it is C/C++.
project (
kProcessor
LANGUAGES CXX C
VERSION 1.1
)
option(BUILD_TESTS "Build tests" OFF)
option(BUILD_APPS "Build kProcessor apps" OFF)
option(BUILD_DOCS "Build documentation" OFF)
option(BUILD_ALL "Build everything!" OFF)
#set(CMAKE_CXX_COMPILER /usr/bin/g++-10)
# IMPORTANT == -FPIC #SDSL-LINKING
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
enable_testing()
include_directories("ThirdParty/CLI")
include_directories("ThirdParty/MQF/include")
include_directories("ThirdParty/json")
include_directories("ThirdParty/sdsl-lite/include")
include_directories("ThirdParty/kmerDecoder/include")
include_directories("ThirdParty/kmerDecoder/lib/parallel_hashmap")
include_directories("ThirdParty/cereal/include")
include_directories("ThirdParty/ntCard/include")
add_subdirectory(ThirdParty/MQF/)
add_subdirectory(ThirdParty/sdsl-lite/)
add_subdirectory(ThirdParty/kmerDecoder)
#set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -std=c++17 -fPIC -pedantic -O0 -g -lprofiler")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -fPIC -pedantic -Ofast")
# set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -std=c++17 -fPIC -pedantic -g ")
# set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -std=c++17 -fPIC -pedantic -Ofast")
set (CMAKE_EXE_LINKER_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS_DEBUG}")
#set (CMAKE_EXE_LINKER_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS_DEBUG} -lprofiler")
find_package(OpenMP)
if (OPENMP_FOUND)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
endif()
include(ExternalProject)
ExternalProject_Add(
libntcard_a
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/ntCard
CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/ntCard/autogen.sh && ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/ntCard/configure --prefix=${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/ntCard/ CXXFLAGS=-fPIC
BUILD_COMMAND make
BUILD_IN_SOURCE 1
)
set(ntcardLib "${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/ntCard/libntcard.a")
set(LIBRARY_NAME
kProcessor
)
file(GLOB kProcessorLibSrc
${CMAKE_CURRENT_SOURCE_DIR}/src/algorithms.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/extend_algorithms.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/batchQuery.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/colorTable.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/kDataFrames/colored_kDataFrame.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/kDataFrames/kDataFrameBMQF.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/kDataFrames/kDataFrame.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/kDataFrames/kDataFrameMAP.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/kDataFrames/kDataFrameMQF.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/kDataFrames/kDataFramePHMAP.cpp
${CMAKE_CURRENT_SOURCE_DIR}/src/Utils/utils.cpp
)
add_library(${LIBRARY_NAME} STATIC
${kProcessorLibSrc}
)
target_link_libraries(kProcessor MQF)
target_link_libraries (kProcessor ${ntcardLib} -ldl)
#set_property(TARGET sdsl PROPERTY POSITION_INDEPENDENT_CODE ON)
target_link_libraries(kProcessor sdsl)
target_link_libraries(kProcessor kmerDecoder)
target_include_directories(${LIBRARY_NAME} PRIVATE
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/${LIBRARY_NAME}>
$<INSTALL_INTERFACE:include/${LIBRARY_NAME}>
)
target_include_directories(${LIBRARY_NAME} PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/${LIBRARY_NAME}>
$<INSTALL_INTERFACE:include/${LIBRARY_NAME}>
)
set(LDFLAGS "-lrt -lpthread -lbz2 -lz")
if(BUILD_ALL)
SET(BUILD_TESTS ON)
# SET(BUILD_APPS ON) # Deferred
SET(BUILD_DOCS ON)
endif()
if(BUILD_TESTS)
add_subdirectory(tests/)
endif()
if(BUILD_APPS)
# add_subdirectory(apps/) # Deferred
message("WARNING: Apps are not available in this release")
endif()
#### Building Documentation with Doxygen
if(BUILD_DOCS)
if(NOT ${DOXYGEN_FOUND})
message(FATAL_ERROR "Doxygen is needed to build the documentation.")
else()
include(cmake/CPM.cmake)
CPMAddPackage(
NAME MCSS
DOWNLOAD_ONLY YES
GITHUB_REPOSITORY mosra/m.css
GIT_TAG 42d4a9a48f31f5df6e246c948403b54b50574a2a
)
# set Doxyfile variables
set(DOXYGEN_PROJECT_NAME kProcessor)
set(DOXYGEN_PROJECT_VERSION ${kProcessor_VERSION})
set(DOXYGEN_PROJECT_ROOT "${CMAKE_CURRENT_LIST_DIR}")
set(DOXYGEN_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
configure_file(${CMAKE_CURRENT_LIST_DIR}/Doxyfile ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
configure_file(${CMAKE_CURRENT_LIST_DIR}/conf.py ${CMAKE_CURRENT_BINARY_DIR}/conf.py)
add_custom_target(
GenerateDocs
${CMAKE_COMMAND} -E make_directory "${DOXYGEN_OUTPUT_DIRECTORY}"
COMMAND "${MCSS_SOURCE_DIR}/documentation/doxygen.py" "${CMAKE_CURRENT_BINARY_DIR}/conf.py"
COMMAND echo "Docs written to: ${DOXYGEN_OUTPUT_DIRECTORY}"
WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
)
endif()
endif()