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project(gatb-core)
# We set the required version
cmake_minimum_required (VERSION 3.10.0)
################################################################################
# The version number.
################################################################################
# The default version number is the latest official build
SET (gatb-core_VERSION_MAJOR 1)
SET (gatb-core_VERSION_MINOR 4)
SET (gatb-core_VERSION_PATCH 2)
# But, it is possible to define another release number during a local build
IF (DEFINED MAJOR)
SET (gatb-core_VERSION_MAJOR ${MAJOR})
ENDIF()
IF (DEFINED MINOR)
SET (gatb-core_VERSION_MINOR ${MINOR})
ENDIF()
IF (DEFINED PATCH)
SET (gatb-core_VERSION_PATCH ${PATCH})
ENDIF()
set (gatb-core-version ${gatb-core_VERSION_MAJOR}.${gatb-core_VERSION_MINOR}.${gatb-core_VERSION_PATCH})
# However, continuous integration has priority over local compilation
IF (DEFINED JENKINS_TAG)
SET (gatb-core-version ${JENKINS_TAG})
ENDIF()
# User login to upload doc-api; Jenkins has priority over local user
IF (DEFINED JENKINS_GFORGE_USER)
SET (gatb-doc-user-login ${JENKINS_GFORGE_USER})
ELSE()
SET (gatb-doc-user-login $ENV{USER})
ENDIF()
set (gatb-core-date "xxxx-xx-xx")
################################################################################
# Define cmake modules directory
################################################################################
set (CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
################################################################################
# Include external cmake files
################################################################################
include (DefineInteger)
include (CppUnit)
# We check whether we have native 128 bits integers
DefineInteger (k)
# We get the current date
string (TIMESTAMP gatb-core-date "%Y-%m-%d/%H:%M:%S")
################################################################################
# COMPILER DEFINITIONS
################################################################################
# We try to find the best compiler config, in particular for C++ extension usage
if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
IF(NOT CMAKE_CXX_COMPILER_VERSION) #for old cmakes
include(CheckCompiler)
ENDIF()
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.7)
message(FATAL_ERROR "Insufficient gcc version (gcc>=4.7 needed)")
endif()
elseif (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
if ("${CMAKE_CXX_COMPILER_VERSION}" STREQUAL "")
# travis-cl has a clang that shows no version, so trying this http://stackoverflow.com/questions/16150888/cmake-branch-on-clang-version
EXECUTE_PROCESS( COMMAND ${CMAKE_CXX_COMPILER} --version OUTPUT_VARIABLE clang_full_version_string )
string (REGEX REPLACE ".*clang version ([0-9]+\\.[0-9]+).*" "\\1" CLANG_VERSION_STRING ${clang_full_version_string})
set(CMAKE_CXX_COMPILER_VERSION ${CLANG_VERSION_STRING})
endif()
IF(CMAKE_SYSTEM_NAME MATCHES "(Darwin)") # different clang versions number between linux and mac
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.3)
message(FATAL_ERROR "Insufficient clang version (clang>=4.5 needed)")
endif()
else()
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.2)
message(FATAL_ERROR "Insufficient clang version (clang>=3.2 needed)")
endif()
endif()
else()
message ("-------------------------------------------------------------------------------------")
message ("-- WARNING !!! YOU USE AN UNKNOWN COMPILER...")
message ("-------------------------------------------------------------------------------------")
endif()
################################################################################
# GENERAL DEFINITIONS
################################################################################
set (LIBRARY_COMPILE_DEFINITIONS "-std=c++11")
set (LIB_COMPILE_WARNINGS "-Wall -Wno-unused-function -Wno-unknown-pragmas") # last one is exclusively for BooPHF
if (CMAKE_BUILD_TYPE STREQUAL "Debug")
set (debug 1)
endif()
if (debug)
#set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -g -p -pg")
set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -g -p ${LIB_COMPILE_WARNINGS}")
set (CMAKE_BUILD_TYPE Debug) # else CMake adds DNDEBUG
message("-- COMPILATION IN DEBUG MODE")
endif()
if (INT128_FOUND)
set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -DINT128_FOUND")
endif()
if (NONCANONICAL)
MESSAGE("--- Compiling with non-canonical (direct strand only) k-mer counting")
set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -DNONCANONICAL=1")
endif()
set(SSE2_FOUND false CACHE BOOL "SSE2 not available")
set(SSE4_2_FOUND false CACHE BOOL "SSE4.2 not available")
# WARNING !!! For the moment, we need to remove some warnings (on Macos) due to use of offsetof macro on non Plain Old Data
set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -Wno-invalid-offsetof")
# We may have some custom compilation flags.
if (use_allocator)
set (LIBRARY_COMPILE_DEFINITIONS "${LIBRARY_COMPILE_DEFINITIONS} -DGATB_USE_CUSTOM_ALLOCATOR")
endif()
message("-- Options: ${LIBRARY_COMPILE_DEFINITIONS}")
################################################################################
# DIRECTORIES MANAGEMENT
################################################################################
set (LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE})
set (EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE})
################################################################################
# EXPORT FOR THIRD PARTIES
################################################################################
# In case you need to use external libraries, you can use the following variables:
# EXTRALIBS : names of the libraries to be used
# EXTRALIBS_PATH : directory where the libraries are
# EXTRALIBS_INC : directory of the include files for the libraries
# For instance, you can do the following:
# cmake -DEXTRALIBS="somelib" -DEXTRALIBS_PATH="/somewhere/libs" -DEXTRALIBS_INC="/somewhere/inc" ..
IF (DEFINED EXTRALIBS)
set (gatb-core-extra-libraries ${EXTRALIBS})
set (gatb-core-extra-libraries ${gatb-core-extra-libraries} PARENT_SCOPE)
ENDIF()
IF (DEFINED EXTRALIBS_PATH)
set (gatb-core-extra-libraries-path ${EXTRALIBS_PATH})
set (gatb-core-extra-libraries-path ${gatb-core-extra-libraries-path} PARENT_SCOPE)
ENDIF()
IF (DEFINED EXTRALIBS_INC)
set (gatb-core-extra-libraries-inc ${EXTRALIBS_INC})
set (gatb-core-extra-libraries-inc ${gatb-core-extra-libraries-inc} PARENT_SCOPE)
ENDIF()
# We define the compilation flags used for compiling binary based on gatb core
set (gatb-core-flags ${LIBRARY_COMPILE_DEFINITIONS})
# We define the include directories used for linking binary based on gatb core
# Note that we need to add boost include dependency (not working otherwise with clang)
set (gatb-core-includes ${PROJECT_BINARY_DIR}/include ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc})
# We define the libraries used for linking binary based on gatb core
set (gatb-core-libraries gatbcore-static dl pthread z ${gatb-core-extra-libraries})
# We define the directory where to find cmake helpers
set (gatb-core-cmake ${CMAKE_MODULE_PATH})
################################################################################
# DEPENDENCIES
################################################################################
# we must be sure that hdf5 is built and installed before building gatb-core
find_package(HDF5 REQUIRED)
include_directories(${HDF5_INCLUDE_DIRS})
# Not sure what exact programs will need these libraries
# see https://lists.debian.org/debian-mentors/2017/11/msg00227.html
# target_link_libraries(name_of_program_or_library ${HDF5_LIBRARIES})
set (gatb-core-libraries ${gatb-core-libraries} ${HDF5_LIBRARIES})
MESSAGE(STATUS HDF5_LIBRARIES="${HDF5_LIBRARIES}")
################################################################################
# LIBRARY GENERATION
################################################################################
ADD_SUBDIRECTORY(src)
# NOTE... we have to duplicate the variables for the other scopes (in particular for sub directories)
set (gatb-core-klist ${gatb-core-klist} PARENT_SCOPE)
################################################################################
# UNIT TESTS GENERATION
################################################################################
IF (DEFINED CPPUNIT_FOUND)
IF (EXISTS "${PROJECT_SOURCE_DIR}/test")
IF (NOT DEFINED GATB_CORE_EXCLUDE_TESTS)
ADD_SUBDIRECTORY (test)
ENDIF()
ENDIF()
ENDIF()
################################################################################
# TOOLS GENERATION
################################################################################
IF (NOT DEFINED GATB_CORE_EXCLUDE_TOOLS)
ADD_SUBDIRECTORY(tools)
ENDIF()
################################################################################
# THIRD PARTY GENERATION (
################################################################################
ADD_SUBDIRECTORY(thirdparty)
# NOTE... we have to duplicate the variables for the other scopes (in particular for sub directories)
set (gatb-core-flags ${gatb-core-flags} PARENT_SCOPE)
set (gatb-core-includes ${gatb-core-includes} PARENT_SCOPE)
set (gatb-core-libraries ${gatb-core-libraries} PARENT_SCOPE)
set (gatb-core-cmake ${gatb-core-cmake} PARENT_SCOPE)
################################################################################
# DOCUMENTATION GENERATION
################################################################################
IF (EXISTS "${PROJECT_SOURCE_DIR}/doc")
ADD_SUBDIRECTORY(doc EXCLUDE_FROM_ALL)
ENDIF()
################################################################################
# EXAMPLES GENERATION
################################################################################
IF (EXISTS "${PROJECT_SOURCE_DIR}/examples")
IF (GATB_CORE_INCLUDE_EXAMPLES)
ADD_SUBDIRECTORY(examples)
ENDIF()
ENDIF()
IF (NOT DEFINED GATB_CORE_EXCLUDE_EXAMPLES)
# add example snippets into binary archive (use by CPack directive)
INSTALL(DIRECTORY "${PROJECT_SOURCE_DIR}/examples/" DESTINATION "share/doc/gatb-core/examples")
ENDIF()
################################################################################
# INSTALL
################################################################################
IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL)
## does not work :-( ## INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt "share/doc/gatb-core" . OPTIONAL)
# INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL)
# INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL)
# INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include)
ENDIF()
################################################################################
# DELIVERY
################################################################################
SET (CPACK_PACKAGE_DESCRIPTION_SUMMARY "gatb-core project")
SET (CPACK_PACKAGE_VENDOR "Genscale team (INRIA)")
SET (CPACK_PACKAGE_VERSION_MAJOR "${gatb-core_VERSION_MAJOR}")
SET (CPACK_PACKAGE_VERSION_MINOR "${gatb-core_VERSION_MINOR}")
SET (CPACK_PACKAGE_VERSION_PATCH "${gatb-core_VERSION_PATCH}")
SET (CPACK_PACKAGE_VERSION "${gatb-core-version}")
SET (CPACK_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME}")
SET (CPACK_GENERATOR "TGZ")
SET (CPACK_SOURCE_GENERATOR "TGZ")
SET (CPACK_SOURCE_IGNORE_FILES
"^${PROJECT_SOURCE_DIR}/build/"
"^${PROJECT_SOURCE_DIR}/.project"
"^${PROJECT_SOURCE_DIR}/.gitignore"
"^${PROJECT_SOURCE_DIR}/doc/design"
"^${PROJECT_SOURCE_DIR}/DELIVERY.md"
)
IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
# We include the module and get all the delivery targets
include (Delivery)
ENDIF ()
|
