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set (RAPMAP_MAIN_SRCS
RapMap.cpp
RapMapSAIndexer.cpp
RapMapUtils.cpp
RapMapSAMapper.cpp
RapMapFileSystem.cpp
RapMapSAIndex.cpp
HitManager.cpp
FastxParser.cpp
rank9b.cpp
stringpiece.cc
xxhash.c
bit_array.c
edlib.cpp
metro/metrohash64.cpp
#RapMapIndex.cpp
#RapMapMapper.cpp
#RapMapIndexer.cpp
)
set (RAPMAP_ALIGN_SRCS
)
set (RAPMAP_LIB_SRCS
)
include_directories(
${GAT_SOURCE_DIR}/include
${GAT_SOURCE_DIR}/digestpp
${GAT_SOURCE_DIR}/external
${GAT_SOURCE_DIR}/external/cereal/include
${GAT_SOURCE_DIR}/external/install/include
${ZLIB_INCLUDE_DIR}
${CEREAL_INCLUDE_DIRS}
)
link_directories(
${GAT_SOURCE_DIR}/lib
${GAT_SOURCE_DIR}/external/install/lib
)
# Set the RPATH
if (NOT APPLE)
set(CMAKE_INSTALL_RPATH "$ORIGIN/../lib:$ORIGIN/../../lib:$ORIGIN/:$ORIGIN/../../external/install/lib")
set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
else()
# use, i.e. don't skip the full RPATH for the build tree
set(CMAKE_SKIP_BUILD_RPATH FALSE)
# when building, don't use the install RPATH already
# (but later on when installing)
set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
# the RPATH to be used when installing
set(CMAKE_INSTALL_RPATH "")
# don't add the automatically determined parts of the RPATH
# which point to directories outside the build tree to the install RPATH
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
endif()
# Build the rapmap executable
add_executable(rapmap ${RAPMAP_MAIN_SRCS})
# our suffix array construction libraries
set (SUFFARRAY_LIB divsufsort)
set (SUFFARRAY64_LIB divsufsort64)
# build KSW2 library
set (KSW2PP_BASIC_LIB_SRCS
ksw2pp/kalloc.c
ksw2pp/ksw2_extd.c
ksw2pp/ksw2_extz.c
ksw2pp/ksw2_gg.c
ksw2pp/ksw2_gg2.c
ksw2pp/ksw2_gg2_sse.c
ksw2pp/KSW2Aligner.cpp
)
set (KSW2PP_ADVANCED_LIB_SRCS
ksw2pp/ksw2_extd2_sse.c
ksw2pp/ksw2_extf2_sse.c
ksw2pp/ksw2_extz2_sse.c
)
# check if we know how to do IPO
check_ipo_supported(RESULT HAS_IPOHAS_IPO)
add_library(ksw2pp_sse2 OBJECT ${KSW2PP_ADVANCED_LIB_SRCS})
add_library(ksw2pp_sse4 OBJECT ${KSW2PP_ADVANCED_LIB_SRCS})
add_library(ksw2pp_basic OBJECT ${KSW2PP_BASIC_LIB_SRCS})
set_target_properties(ksw2pp_sse2 PROPERTIES COMPILE_FLAGS "-O3 -msse2 -mno-sse4.1")
set_target_properties(ksw2pp_sse2 PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;KSW_SSE2_ONLY;HAVE_KALLOC")
set_target_properties(ksw2pp_sse4 PROPERTIES COMPILE_FLAGS "-O3 -msse4.1")
set_target_properties(ksw2pp_sse4 PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")
set_target_properties(ksw2pp_basic PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")
set_target_properties(ksw2pp_basic PROPERTIES INCLUDE_DIRECTORIES ${GAT_SOURCE_DIR}/include)
set_target_properties(ksw2pp_sse4 PROPERTIES INCLUDE_DIRECTORIES ${GAT_SOURCE_DIR}/include)
# Build the ksw2pp library
add_library(ksw2pp STATIC $<TARGET_OBJECTS:ksw2pp_sse2> $<TARGET_OBJECTS:ksw2pp_sse4> $<TARGET_OBJECTS:ksw2pp_basic>)
set_target_properties(ksw2pp PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")
if(HAS_IPO)
set_property(TARGET ksw2pp PROPERTY INTERPROCEDURAL_OPTIMIZATION True)
endif()
# Link the executable
target_link_libraries(rapmap
# ${PTHREAD_LIB}
${ZLIB_LIBRARY}
${SUFFARRAY_LIB}
${SUFFARRAY64_LIB}
m
${NON_APPLECLANG_LIBS}
${FAST_MALLOC_LIB}
${CMAKE_THREAD_LIBS_INIT}
${LIBRT}
ksw2pp
${CMAKE_DL_LIBS}
#${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
#${LIBLZMA_LIBRARIES}
)
##
# External dependencies of salmon_core and salmon
##
if (${FETCHED_JEMALLOC})
add_dependencies(rapmap libjemalloc)
add_dependencies(rapmap libjemalloc)
endif()
##### ======================================
IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
SET(CMAKE_INSTALL_PREFIX
"${GAT_SOURCE_DIR}" CACHE PATH "Default install prefix" FORCE
)
ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(INSTALL_LIB_DIR lib )
set(INSTALL_BIN_DIR bin )
set(INSTALL_INCLUDE_DIR include )
# install(FILES ${Boost_LIBRARIES}
# DESTINATION ${INSTALL_LIB_DIR})
install(TARGETS rapmap
RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib
)
install(FILES ${GAT_SOURCE_DIR}/scripts/RunRapMap.sh
PERMISSIONS WORLD_EXECUTE WORLD_READ OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
DESTINATION bin)
#set(POST_INSTALL_SCRIPT ${GAT_SOURCE_DIR}/cmake/PostInstall.cmake)
#install(
# CODE
# "
# execute_process(COMMAND \"${CMAKE_COMMAND}\"
# -DCMAKE_SYSTEM_NAME=${CMAKE_SYSTEM_NAME}
# -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
# -P \"${POST_INSTALL_SCRIPT}\")
# "
#)
#
#include(InstallRequiredSystemLibraries)
add_test( NAME quasi_map_test COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestQuasiMap.cmake )
add_test( NAME quasi_map_test_ph COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestQuasiMapPerfectHash.cmake )
|
