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|
cmake_minimum_required(VERSION 2.8)
cmake_policy(SET CMP0048 NEW)
cmake_policy(SET CMP0005 NEW)
file(STRINGS ${CMAKE_SOURCE_DIR}/BOWTIE2_VERSION PROJECT_VERSION)
project(bowtie2 LANGUAGES CXX VERSION ${PROJECT_VERSION})
enable_testing()
include(CTest)
include(ExternalProject)
include(ProcessorCount)
include(CheckSymbolExists)
ProcessorCount(NUM_CORES)
option(BOWTIE_MM "enable bowtie2 memory mapping" ON)
option(BOWITE_SHARED_MM "enable shared memory mapping" ON)
set(NO_TBB ${NO_TBB})
set(NO_SPINLOCK ${NO_SPINLOCK})
set(USE_SRA ${USE_SRA})
set(WITH_THREAD_PROFILING ${WITH_THREAD_PROFILING})
set(NO_POPCNT_CAPABILITY ${NO_POPCNT_CAPABILITY})
set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 -g3 -Wall -msse2")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -funroll-loops")
set(INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
set(CMAKE_EXPORT_COMPILE_COMMANDS on)
if (MINGW)
option(BOWTIE_MM "Memory mapped files not supported on Windows" OFF)
option(BOWTIE_SHARED_MEM "Shared memory not supported on Windows" OFF)
endif(MINGW)
if (APPLE)
set(CMAKE_XCODE_ATTRIBUTE_DEBUG_INFORMATION_FORMAT "dwarf-with-dsym")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
endif(APPLE)
set(BOWTIE2_BIN_LIST
bowtie2-build-s
bowtie2-build-l
bowtie2-align-s
bowtie2-align-l
bowtie2-inspect-s
bowtie2-inspect-l
)
set(BOWTIE2_WRAPPER_SCRIPTS
bowtie2
bowtie2-build
bowtie2-inspect
)
set(SHARED_CPPS
ccnt_lut.cpp
ref_read.cpp
alphabet.cpp
shmem.cpp
edit.cpp
bt2_idx.cpp
bt2_io.cpp
bt2_util.cpp
reference.cpp
ds.cpp
multikey_qsort.cpp
limit.cpp
random_source.cpp
)
set(SEARCH_CPPS
qual.cpp pat.cpp sam.cpp
read_qseq.cpp aligner_seed_policy.cpp
aligner_seed.cpp
aligner_seed2.cpp
aligner_sw.cpp
aligner_sw_driver.cpp aligner_cache.cpp
aligner_result.cpp ref_coord.cpp mask.cpp
pe.cpp aln_sink.cpp dp_framer.cpp
scoring.cpp presets.cpp unique.cpp
simple_func.cpp
random_util.cpp
aligner_bt.cpp sse_util.cpp
aligner_swsse.cpp outq.cpp
aligner_swsse_loc_i16.cpp
aligner_swsse_ee_i16.cpp
aligner_swsse_loc_u8.cpp
aligner_swsse_ee_u8.cpp
aligner_driver.cpp
bowtie_main.cpp
bt2_search.cpp
)
set(BUILD_CPPS
bt2_build.cpp
diff_sample.cpp
bowtie_build_main.cpp)
set(INSPECT_CPPS
bt2_inspect.cpp
)
string(TIMESTAMP BUILD_DATE)
execute_process(COMMAND ${CMAKE_CXX_COMPILER} -v OUTPUT_VARIABLE COMPILER_VERSION)
add_definitions(
-DBOWTIE2
-DBUILD_HOST="${CMAKE_HOST_SYSTEM}"
-DBUILD_TIME="${BUILD_DATE}"
-DCOMPILER_VERSION="${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_VERSION}"
-DBOWTIE2_VERSION="${PROJECT_VERSION}"
-D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64
-D_GNU_SOURCE
)
if (WITH_AFFINITY)
add_definitions(-DWITH_AFFINITY=1)
endif()
if (NO_SPINLOCK)
add_definitions(-DNO_SPINLOCK)
endif()
if (NOT NO_POPCNT_CAPABILITY)
add_definitions(-DPOPCNT_CAPABILITY)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -I third_party")
endif()
if (USE_SRA)
set(NGS_VER 2.9.2)
set(NCBI_VDB_VER 2.9.2-1)
find_package(Java COMPONENTS Development REQUIRED)
find_package(PythonInterp REQUIRED)
find_package(Perl REQUIRED)
find_program(MAKE_EXE NAMES gmake nmake make)
ExternalProject_add(ngs_project
URL https://github.com/ncbi/ngs/archive/${NGS_VER}.tar.gz
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ngs-${NGS_VER}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND ./configure --prefix=install
BUILD_COMMAND ${MAKE_EXE}
INSTALL_COMMAND ${MAKE_EXE} install
)
ExternalProject_Get_Property(ngs_project SOURCE_DIR)
set(NGS_INSTALL_DIR ${SOURCE_DIR}/ngs-sdk/install)
link_directories(${NGS_INSTALL_DIR}/lib64)
include_directories(${NGS_INSTALL_DIR}/include)
add_library(ngs-c++-static STATIC IMPORTED)
add_dependencies(ngs-c++-static ngs_project)
find_library(LIBNGS_CPP ngs-c++-static PATHS ${NGS_INSTALL_DIR}/lib64 NO_DEFAULT_PATH)
set_property(TARGET ngs-c++-static PROPERTY IMPORTED_LOCATION ${LIBNGS_CPP})
link_libraries(ngs-c++-static)
ExternalProject_add(ncbi_vdb_project
URL https://github.com/ncbi/ncbi-vdb/archive/${NCBI_VDB_VER}.tar.gz
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ncbi-vdb-${NCBI_VDB_VER}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND ./configure --prefix=install --with-ngs-sdk=${NGS_INSTALL_DIR}
BUILD_COMMAND ${MAKE_EXE}
INSTALL_COMMAND ${MAKE_EXE} install
DEPENDS ngs_project
)
ExternalProject_Get_Property(ncbi_vdb_project SOURCE_DIR)
set(NCBI_VDB_INSTALL_DIR ${SOURCE_DIR}/install)
link_directories(${NCBI_VDB_INSTALL_DIR}/lib64)
include_directories(${NCBI_VDB_INSTALL_DIR}/include)
add_library(ncbi-ngs-c++-static STATIC IMPORTED)
add_dependencies(ncbi-ngs-c++-static ncbi_vdb_project)
find_library(LIBNCBI_NGS_CPP ncbi-ngs-c++-static PATHS ${NCBI_VDB_INSTALL_DIR}/lib64 NO_DEFAULT_ATH)
set_property(TARGET ncbi-ngs-c++-static PROPERTY IMPORTED_LOCATION ${LIBNCBI_NGS_CPP})
add_library(ncbi-vdb-static STATIC IMPORTED)
add_dependencies(ncbi-vdb-static ncbi_vdb_project)
find_library(LIBNCBI_VDB ncbi-vdb-static PATHS ${NCBI_VDB_INSTALL_DIR}/lib64 NO_DEFAULT_PATH)
set_property(TARGET ncbi-vdb-static PROPERTY IMPORTED_LOCATION ${LIBNCBI_VDB})
link_libraries(ncbi-ngs-c++-static ncbi-vdb-static)
add_definitions(-DUSE_SRA)
endif()
if (WITH_THREAD_PROFILING)
add_definitions(-DPER_THREAD_TIMING=1)
endif()
if (CMAKE_BUILD_TYPE STREQUAL "Release")
add_definitions(-DNDEBUG)
endif()
find_package(ZLIB REQUIRED)
find_package(Threads REQUIRED)
link_libraries(Threads::Threads)
if (NO_TBB)
set(SHARED_CPPS ${SHARED_CPPS} tinythread.cpp)
else()
find_library(TBB_LIB_PATH tbb)
if (TBB_LIB_PATH)
find_path(TBB_INCLUDE_PATH tbb/tbb.h)
link_libraries(${TBB_LIB_PATH})
find_library(TBBMALLOC_PROXY_LIB_PATH tbbmalloc_proxy)
if (NOT TBBMALLOC_PROXY_LIB_PATH)
find_library(TBBMALLOC_LIB_PATH tbbmalloc)
link_libraries(${TBBMALLOC_LIB_PATH})
else()
link_libraries(${TBBMALLOC_PROXY_LIB_PATH})
endif()
include_directories(${TBB_INCLUDE_PATH})
else()
set(TBB_VER 2019_U4)
if (CMAKE_SYSTEM_NAME STREQUAL Linux)
set(tbb_os linux)
elseif (CMAKE_SYSTEM_NAME STREQUAL Darwin)
set(tbb_os macos)
elseif (CMAKE_SYSTEM_NAME STREQUAL Windows)
set(tbb_os windows)
else()
set(tbb_os ${CMAKE_SYSTEM_NAME})
endif()
find_program(MAKE_EXE NAMES gmake nmake make)
ExternalProject_Add(tbb_project
URL https://github.com/01org/tbb/archive/2019_U4.tar.gz
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/tbb-${TBB_VER}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND ""
BUILD_COMMAND ${MAKE_EXE} tbb_build_prefix=${TBB_VER} tbb_os=${tbb_os}
INSTALL_COMMAND ""
PREFIX=${CMAKE_CURRENT_BINARY_DIR}/tbb_project
)
ExternalProject_Get_Property(tbb_project SOURCE_DIR)
set(TBB_SOURCE_DIR ${SOURCE_DIR})
set(TBB_RELEASE_DIR ${TBB_SOURCE_DIR}/build/${TBB_VER}_release)
include_directories(${TBB_SOURCE_DIR}/include)
find_path(TBB_INCLUDE_PATH PATHS ${TBB_SOURCE_DIR}/include NAMES tbb/tbb.h)
link_directories(${TBB_RELEASE_DIR})
add_library(tbb SHARED IMPORTED)
add_dependencies(tbb tbb_project)
find_library(LIBTBB tbb PATHS ${TBB_RELEASE_DIR} NO_DEFAULT_PATH)
set_property(TARGET tbb PROPERTY IMPORTED_LOCATION ${LIBTBB})
add_library(tbbmalloc_proxy SHARED IMPORTED)
add_dependencies(tbbmalloc_proxy tbb_project)
find_library(LIBTBBMALLOC_PROXY tbbmalloc_proxy PATHS ${TBB_RELEASE_DIR} NO_DEFAULT_PATH)
if (NOT LIBTBBMALLOC_PROXY)
add_library(tbbmalloc SHARED IMPORTED)
add_dependencies(tbbmalloc tbb_project)
find_library(LIBTBBMALLOC tbbmalloc PATHS ${TBB_RELEASE_DIR} NO_DEFAULT_PATH)
set_property(TARGET tbbmalloc PROPERTY IMPORTED_LOCATION ${LIBTBBMALLOC})
link_libraries(tbb tbbmalloc)
else()
set_property(TARGET tbbmalloc_proxy PROPERTY IMPORTED_LOCATION ${LIBTBBMALLOC_PROXY})
link_libraries(tbb tbbmalloc_proxy)
endif()
endif()
add_definitions(-DWITH_TBB -DWITH_QUEUELOCK=1 -DNO_SPINLOCK)
endif()
if (ZLIB_FOUND)
link_libraries(${ZLIB_LIBRARIES})
include_directories(${ZLIB_INCLUDE_DIRS})
endif()
include_directories(${PROJECT_SOURCE_DIR})
get_directory_property(COMPILER_DEFS COMPILE_DEFINITIONS)
string(REGEX REPLACE "-fdebug-prefix-map=[^ ]* " "" COMP_OPTS ${CMAKE_CXX_FLAGS})
string(REGEX REPLACE "-ffile-prefix-map=[^ ]* " "" COMP_OPTS ${COMP_OPTS})
add_definitions(-DCOMPILER_OPTIONS="${COMP_OPTS}")
add_executable(bowtie2-align-s ${SEARCH_CPPS} ${SHARED_CPPS})
add_executable(bowtie2-align-l ${SEARCH_CPPS} ${SHARED_CPPS})
add_executable(bowtie2-build-s ${BUILD_CPPS} ${SHARED_CPPS})
add_executable(bowtie2-build-l ${BUILD_CPPS} ${SHARED_CPPS})
add_executable(bowtie2-inspect-s ${INSPECT_CPPS} ${SHARED_CPPS})
add_executable(bowtie2-inspect-l ${INSPECT_CPPS} ${SHARED_CPPS})
set_target_properties(bowtie2-align-l bowtie2-build-l bowtie2-inspect-l PROPERTIES COMPILE_FLAGS "-DBOWTIE2_64BIT_INDEX")
set_target_properties(bowtie2-inspect-s bowtie2-inspect-l PROPERTIES COMPILE_FLAGS "-DBOWTIE_INSPECT_MAIN")
# set_target_properties(${BOWTIE2_BIN_LIST} PROPERTIES DEBUG_POSTFIX -debug)
install(TARGETS ${BOWTIE2_BIN_LIST} DESTINATION bin)
install(FILES ${BOWTIE2_WRAPPER_SCRIPTS}
PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
DESTINATION bin)
if (LIBTBB)
install(FILES ${LIBTBB} DESTINATION lib)
install(DIRECTORY ${TBB_INCLUDE_PATH} DESTINATION include)
endif()
if (LIBTBBMALLOC)
install(FILES ${LIBTBBMALLOC} DESTINATION lib)
endif()
if (LIBTBBMALLOC_PROXY)
install(FILES ${LIBTBBMALLOC_PROXY} DESTINATION lib)
endif()
add_test(NAME simple-align
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
COMMAND bowtie2 -x example/index/lambda_virus example/reads/longreads.fq -u 10)
add_test(NAME simple-build
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
COMMAND bowtie2-build-s -c GGGCGGCGACCTCGCGGGTTTTCGCTA out)
add_test(NAME simple-inspect
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
COMMAND bowtie2-inspect-s out && rm out*)
|
