https://github.com/kdmurray91/kWIP
Revision c8bec26c8e1efefc01a9686b3ab9297c192548f6 authored by Kevin Murray on 27 January 2019, 08:03:47 UTC, committed by Kevin Murray on 27 January 2019, 08:03:47 UTC
1 parent 3cf8a9e
Tip revision: c8bec26c8e1efefc01a9686b3ab9297c192548f6 authored by Kevin Murray on 27 January 2019, 08:03:47 UTC
Update link to published paper
Update link to published paper
Tip revision: c8bec26
CMakeLists.txt
CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
PROJECT(kwip)
###############
# Cmake Blerg #
###############
# Find the modules
LIST(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
# Set sane output paths
SET(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
LINK_DIRECTORIES(${CMAKE_BINARY_DIR}/lib)
ENABLE_TESTING()
# Default to Release builds
IF (NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE Release)
ENDIF()
# Version jiggery-pokery
IF ("${KWIP_VERSION}") # Manually set the version
SET(VERSION "${KWIP_VERSION}")
ELSE()
# git describe as versioning
EXECUTE_PROCESS(COMMAND git describe --always
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
OUTPUT_VARIABLE VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE)
ENDIF()
MESSAGE(STATUS "${CMAKE_BUILD_TYPE} build of ${PROJECT_NAME} version: ${VERSION}")
############################
## User-definable options ##
############################
OPTION(ENABLE_ASAN "Build with AddressSanitizer" OFF)
OPTION(UNSAFE_MATH "Use -ffast-math in Release build? (costs a little accuracy)" ON)
OPTION(ENABLE_TSAN "Build with ThreadSanitizer" OFF)
OPTION(USE_OPENMP "Use OpenMP for parallelism" ON)
OPTION(USE_SYSTEM_KHMER "Use a globally pre-installed copy of khmer" OFF)
###############################
## Find Packages and Headers ##
###############################
IF (USE_SYSTEM_KHMER)
FIND_PACKAGE(oxli 2.0 REQUIRED)
SET(KMERCLUST_DEPENDS_LIBS ${KMERCLUST_DEPENDS_LIBS} ${OXLI_LIBRARIES})
INCLUDE_DIRECTORIES(${OXLI_INCLUDE_DIRS})
ELSE()
INCLUDE_DIRECTORIES(src/ext)
INCLUDE_DIRECTORIES(src/ext/seqan/core/include)
ENDIF ()
FIND_PACKAGE(ZLIB 1.2.3 REQUIRED)
INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIRS})
SET(KMERCLUST_DEPENDS_LIBS ${KMERCLUST_DEPENDS_LIBS} ${ZLIB_LIBRARIES})
FIND_PACKAGE(Eigen3 3.0.0 REQUIRED)
INCLUDE_DIRECTORIES(${EIGEN3_INCLUDE_DIR})
# Eigen is header only, no need for libs
SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${ZLIB_C_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ZLIB_C_FLAGS} -DSEQAN_HAS_ZLIB=1")
IF(USE_OPENMP)
FIND_PACKAGE(OpenMP)
IF(OPENMP_FOUND)
SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
ENDIF()
ENDIF()
##########################
## Set Compiler Options ##
##########################
# Set CFLAGS
SET(WARN_FLAGS "${WARN_FLAGS} -Wall -Wextra -Wno-ignored-qualifiers")
SET(OPT_FLAGS "${OPT_FLAGS} -march=native")
SET(REL_OPT_FLAGS "-O3")
IF(UNSAFE_MATH)
SET(REL_OPT_FLAGS "-ffast-math -Ofast")
ENDIF()
IF(ENABLE_ASAN AND ENABLE_TSAN)
MESSAGE(FATAL_ERROR "Cannot enable both ThreadSanitizer and AddressSanitizer")
ENDIF()
IF(ENABLE_ASAN)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address")
ENDIF()
IF(ENABLE_TSAN)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread -fPIC -pie")
ENDIF()
SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11 ${WARN_FLAGS} ${OPT_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 ${WARN_FLAGS} ${OPT_FLAGS}")
SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${REL_OPT_FLAGS}")
# Headers occur in these dirs
INCLUDE_DIRECTORIES(${CMAKE_BINARY_DIR}
${CMAKE_SOURCE_DIR}/src
${CMAKE_SOURCE_DIR}/tests
${CMAKE_SOURCE_DIR}/tests/ext)
# Finally, configure the config header
CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/src/kwip-config.hh.in
${CMAKE_BINARY_DIR}/kwip-config.hh)
# Libary sources
ADD_SUBDIRECTORY(src)
ADD_SUBDIRECTORY(tests)
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