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CMakeLists.txt
118 lines (95 loc) · 5.07 KB
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CMakeLists.txt
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cmake_minimum_required(VERSION 2.8)
project(megahit)
set(CMAKE_VERBOSE_MAKEFILE ON)
if (CMAKE_VERSION VERSION_LESS "3.1")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
else ()
set(CMAKE_CXX_STANDARD 11)
endif ()
option(COVERAGE "Generate coverage report" OFF)
option(STATIC_BUILD "Build static executation" OFF)
option(SANITIZER "Enable sanitizers" OFF)
option(TSAN "Enable thread sanitizers" OFF)
include_directories(src)
FILE(GLOB_RECURSE ASMBL_SOURCE "src/assembly/*.cpp")
FILE(GLOB_RECURSE LCASM_SOURCE "src/localasm/*.cpp")
FILE(GLOB_RECURSE IDBA_SOURCE "src/idba/*.cpp")
FILE(GLOB_RECURSE SDBG_SOURCE "src/sdbg/*.cpp")
FILE(GLOB_RECURSE CX1_SOURCE "src/sorting/*.cpp")
FILE(GLOB_RECURSE SEQ_SOURCE "src/sequence/*.cpp")
FILE(GLOB_RECURSE TOOLKIT_SOURCE "src/tools/*.cpp")
LIST(APPEND OTHER_SOURCE
src/main.cpp
src/main_assemble.cpp
src/main_buildlib.cpp
src/main_iterate.cpp
src/main_local_assemble.cpp
src/main_sdbg_build.cpp
src/utils/options_description.cpp
)
if (STATIC_BUILD)
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
endif (STATIC_BUILD)
find_package(ZLIB REQUIRED)
find_package(OpenMP REQUIRED)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DXXH_INLINE_ALL -ftemplate-depth=3000")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unused-function")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprefetch-loop-arrays -funroll-loops")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__XROOT__='\"${CMAKE_SOURCE_DIR}/src\"'")
#set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D__XFILE__='\"$(subst ${CMAKE_SOURCE_DIR}/,,$(abspath $<))\"'")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${ZLIB_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
set(CMAKE_CXX_FLAGS_DEBUG "-g -ggdb -O1 -D_LIBCPP_DEBUG -D_GLIBCXX_DEBUG")
if (COVERAGE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -O0 --coverage")
set(COV_PY "coverage run")
endif (COVERAGE)
if (SANITIZER)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fsanitize=leak -fsanitize=undefined")
endif (SANITIZER)
if (TSAN)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread")
endif (TSAN)
message(STATUS "Build type: ${CMAKE_BUILD_TYPE}: ${CMAKE_CXX_FLAGS}")
add_executable(megahit_core ${OTHER_SOURCE} ${ASMBL_SOURCE} ${IDBA_SOURCE} ${SDBG_SOURCE} ${LCASM_SOURCE} ${SEQ_SOURCE}
${CX1_SOURCE} ${TOOLKIT_SOURCE})
add_executable(megahit_core_popcnt ${OTHER_SOURCE} ${ASMBL_SOURCE} ${IDBA_SOURCE} ${SDBG_SOURCE} ${LCASM_SOURCE} ${SEQ_SOURCE}
${CX1_SOURCE} ${TOOLKIT_SOURCE})
add_executable(megahit_core_no_hw_accel ${OTHER_SOURCE} ${ASMBL_SOURCE} ${IDBA_SOURCE} ${SDBG_SOURCE} ${LCASM_SOURCE}
${SEQ_SOURCE} ${CX1_SOURCE} ${TOOLKIT_SOURCE})
set_target_properties(megahit_core PROPERTIES COMPILE_FLAGS "-mbmi2 -DUSE_BMI2 -mpopcnt")
set_target_properties(megahit_core_popcnt PROPERTIES COMPILE_FLAGS "-mpopcnt")
if (STATIC_BUILD)
# TODO dirty
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -static")
set_target_properties(megahit_core megahit_core_popcnt megahit_core_no_hw_accel PROPERTIES LINK_SEARCH_START_STATIC ON)
set_target_properties(megahit_core megahit_core_popcnt megahit_core_no_hw_accel PROPERTIES LINK_SEARCH_END_STATIC ON)
endif (STATIC_BUILD)
target_link_libraries(megahit_core ${ZLIB_LIBRARIES})
target_link_libraries(megahit_core_popcnt ${ZLIB_LIBRARIES})
target_link_libraries(megahit_core_no_hw_accel ${ZLIB_LIBRARIES})
add_custom_target(
megahit ALL
COMMAND cp ${CMAKE_SOURCE_DIR}/src/megahit .
)
add_custom_target(megahit_toolkit ALL
COMMAND ${CMAKE_COMMAND} -E create_symlink megahit_core_no_hw_accel megahit_toolkit)
set(TEST_DATA ${CMAKE_SOURCE_DIR}/test_data)
add_custom_target(
simple_test
COMMAND ./megahit --test -t 2
COMMAND MEGAHIT_NUM_MERCY_FACTOR=1.5 ./megahit --test -t 4 --mem-flag 0 --no-hw-accel
COMMAND ./megahit --test -t 2 --kmin-1pass --prune-level 3 --prune-depth 0
COMMAND rm -rf test-random && python3 ${TEST_DATA}/generate_random_fasta.py > random.fa && ./megahit -r random.fa --k-list 255 --min-count 1 -o test-random
COMMAND rm -rf test-fastg && ./megahit --test -t 2 --mem-flag 2 --keep-tmp-files -o test-fastg
COMMAND rm -rf test-empty && ./megahit -r ${TEST_DATA}/empty.fa -o test-empty
COMMAND rm -rf test-no-contig && ./megahit -r ${TEST_DATA}/r4.fa -o test-no-contig
COMMAND ./megahit_toolkit contig2fastg 59 test-fastg/intermediate_contigs/k59.contigs.fa > 59.fastg
COMMAND ./megahit_toolkit readstat < test-fastg/intermediate_contigs/k59.contigs.fa
)
add_dependencies(megahit megahit_core megahit_core_popcnt megahit_core_no_hw_accel megahit_toolkit)
add_dependencies(simple_test megahit)
install(TARGETS megahit_core megahit_core_popcnt megahit_core_no_hw_accel DESTINATION bin)
install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/megahit ${CMAKE_CURRENT_BINARY_DIR}/megahit_toolkit DESTINATION bin)
install(DIRECTORY test_data DESTINATION share/${PROJECT_NAME})