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cmake_minimum_required(VERSION 3.16)
project(shastaDynamicExecutable)
# C++ dialect.
add_definitions(-std=c++20)
# Compilation warnings.
add_definitions(-Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -Wunused-parameter)
# Optimization and debug options.
if(BUILD_DEBUG)
add_definitions(-ggdb3)
add_definitions(-O0)
# Address sanitizer does not work well with the Python API,
# so it is commented out here. But it could be useful
# to debug the dynamic executable.
# add_definitions(-fsanitize=address)
else(BUILD_DEBUG)
add_definitions(-O3)
# NDEBUG is required to turn off SeqAn debug code.
add_definitions(-DNDEBUG)
endif(BUILD_DEBUG)
# 16-byte compare and swap.
# This is recommended for dset64.hpp/dset64-gccAtomic.hpp".
# It's available only on x86 architectures.
if(X86_64)
add_definitions(-mcx16)
endif()
# Native build.
if(BUILD_NATIVE)
add_definitions(-march=native)
endif(BUILD_NATIVE)
# Build id.
add_definitions(-DBUILD_ID=${BUILD_ID})
# Definitions needed to eliminate dependency on the boost system library.
add_definitions(-DBOOST_SYSTEM_NO_DEPRECATED)
add_definitions(-DBOOST_ERROR_CODE_HEADER_ONLY)
# This is needed to avoid some Boost warnings about deprecated messages.
# We canot fix this in Shasta as it is a Boost problem.
# It can be removed if Boost is fixed.
add_definitions(-DBOOST_ALLOW_DEPRECATED_HEADERS)
add_definitions(-DSHASTA_PYTHON_API)
# Source files
file(GLOB SOURCES ../srcMain/*.cpp)
# Include directory.
include_directories(../src)
# Define our executable.
add_executable(shastaDynamicExecutable ${SOURCES})
set_target_properties(shastaDynamicExecutable PROPERTIES OUTPUT_NAME "shastaDynamic")
# This is needed to make sure the executable looks for the shared
# library in the same directory.
set_target_properties(shastaDynamicExecutable PROPERTIES INSTALL_RPATH "\$ORIGIN")
# Libraries to link with.
if(X86_64)
target_link_libraries(
shastaDynamicExecutable
shastaDynamicLibrary
atomic boost_system boost_program_options boost_chrono boost_serialization spoa png z
lapack blas quadmath pthread)
else(X86_64)
target_link_libraries(
shastaDynamicExecutable
shastaDynamicLibrary
atomic boost_system boost_program_options boost_chrono boost_serialization spoa png z
lapack blas pthread)
endif(X86_64)
if(BUILD_DEBUG)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsanitize=address")
endif(BUILD_DEBUG)
# Install the dynamic executable into the bin directory.
install(TARGETS shastaDynamicExecutable DESTINATION shasta-install/bin)
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