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|
# ============================================================================
# SeqAn - The Library for Sequence Analysis
# ============================================================================
# Copyright (c) 2006-2018, Knut Reinert, FU Berlin
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Knut Reinert or the FU Berlin nor the names of
# its contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
# OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
# DAMAGE.
# ============================================================================
# Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
# ============================================================================
# This CMake file defines the necessary macros for the SeqAn build system.
#
# Note that while the SeqAn build system uses the seqan-config.cmake module,
# the seqan-config.cmake module itself can be used independently from the SeqAn
# build system.
# ============================================================================
# ----------------------------------------------------------------------------
# Set CMAKE policies.
# ----------------------------------------------------------------------------
if (POLICY CMP0054) # Disables auto-dereferencing of variables in quoted statements
cmake_policy(SET CMP0054 NEW)
endif()
# Valid values for SEQAN_BUILD_SYSTEM:
#
# DEVELOP
# SEQAN_RELEASE_APPS
# SEQAN_RELEASE_LIBRARY
# APP:${app_name}
# require python 2.7, not python3
set(PythonInterp_FIND_VERSION 2.7)
set(PythonInterp_FIND_VERSION_MAJOR 2)
set(PythonInterp_FIND_VERSION_MINOR 7)
set(PythonInterp_FIND_VERSION_COUNT 2)
include (SeqAnUsabilityAnalyzer)
include (CheckCXXCompilerFlag)
if (DEFINED CMAKE_INSTALL_DOCDIR)
set(CMAKE_INSTALL_DOCDIR_IS_SET ON)
endif ()
include (GNUInstallDirs)
set (COMPILER_CLANG FALSE)
set (COMPILER_GCC FALSE)
set (COMPILER_LINTEL FALSE)
set (COMPILER_WINTEL FALSE)
set (COMPILER_MSVC FALSE)
set (STDLIB_VS ${MSVC})
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
set (COMPILER_CLANG TRUE)
elseif (CMAKE_CXX_COMPILER_ID MATCHES "Intel" AND STDLIB_VS)
set (COMPILER_WINTEL TRUE)
elseif (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
set (COMPILER_LINTEL TRUE)
elseif (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
set (COMPILER_GCC TRUE)
elseif (CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
set (COMPILER_MSVC TRUE)
endif ()
# ---------------------------------------------------------------------------
# Enable /bigobj flag on Windows.
# ---------------------------------------------------------------------------
# We need the /bigobj switch on windows (for 64 bit builds only actually).
# Set target system to be Windows Vista and later.
if (COMPILER_MSVC OR COMPILER_WINTEL)
# Set /bigobj for COMPILER_MSVC and COMPILER_WINTEL, but COMPILER_CLANG on
# windows (clang/c2 3.7) can not handle it.
add_definitions (/bigobj)
endif()
if (STDLIB_VS)
add_definitions (-D_WIN32_WINNT=0x0600 -DWINVER=0x0600)
endif ()
# ---------------------------------------------------------------------------
# Is it a 32 bit platform?
# ---------------------------------------------------------------------------
if (CMAKE_SIZEOF_VOID_P EQUAL 4)
set(SEQAN_32BIT_TARGET_PLATFORM 1)
set(SEQAN_64BIT_TARGET_PLATFORM 0)
else()
set(SEQAN_32BIT_TARGET_PLATFORM 0)
set(SEQAN_64BIT_TARGET_PLATFORM 1)
endif()
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
# Disable false positive terminal detection in Xcode
# ---------------------------------------------------------------------------
if (CMAKE_GENERATOR STREQUAL Xcode)
add_definitions (-DSEQAN_NO_TERMINAL)
endif (CMAKE_GENERATOR STREQUAL Xcode)
# ---------------------------------------------------------------------------
# Function add_executable (name [WIN32] [MACOSX_BUNDLE] [EXCLUDE_FROM_ALL]
# source1 source2 ... sourceN)
#
# Add an executable with the given name and sources.
#
# We overwrite the built-in function add_executable to automatically add
# behaviour that is required in the SeqAn build system. This includes:
#
# * Adding dependencies to the SeqAn library headers.
# * Enabling the SeqAn Usability Analyzer (SUA).
#
# Note that it is not possible to overwrite the same function two times.
# ---------------------------------------------------------------------------
function (add_executable NAME)
# Call overwritten _add_executable.
_add_executable(${ARGV})
# Add dependencies on the SeqAn library.
add_dependencies(${NAME} seqan_library)
# Add dependency on the SUA target.
seqan_add_sua_dependency (${NAME})
endfunction (add_executable)
# ---------------------------------------------------------------------------
# Macro seqan_register_apps ()
#
# Register all apps by adding their subdirectories if they are to be built
# (SEQAN_RELEASE and APP:${app} modes).
# ---------------------------------------------------------------------------
macro (seqan_register_apps)
# Get all direct entries of the current source directory into ENTRIES.
file (GLOB ENTRIES
RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_SOURCE_DIR}/[!.]*)
# Add all values from ${ENTRIES} that are subdirectories and have a file
# CMakeListst.txt.
foreach (ENTRY ${ENTRIES})
if (IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY})
if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY}/CMakeLists.txt)
if ((("${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP") OR
("${SEQAN_BUILD_SYSTEM}" STREQUAL "SEQAN_RELEASE_APPS") OR
("${SEQAN_BUILD_SYSTEM}" STREQUAL "APP:${ENTRY}")) AND
(NOT (${${ENTRY}_NO_BUILD})))
add_subdirectory(${ENTRY})
endif ()
endif (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY}/CMakeLists.txt)
endif (IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY})
endforeach (ENTRY ${ENTRIES})
endmacro (seqan_register_apps)
# ---------------------------------------------------------------------------
# Macro seqan_build_system_init ()
#
# Initialize build system.
# ---------------------------------------------------------------------------
macro (seqan_build_system_init)
# Enable CTest and command add_test().
enable_testing ()
# GENERAL SETUP
set (_CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/include")
set (CMAKE_INCLUDE_PATH ${_CMAKE_INCLUDE_PATH} CACHE STRING "")
set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1")
set (SeqAn_DIR ${SeqAn_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake")
# set (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DSEQAN_ENABLE_DEBUG=1" PARENT_SCOPE)
# Enable global exception handler for all "official" stuff
set (SEQAN_DEFINITIONS "${SEQAN_DEFINITIONS} -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1")
set (CMAKE_RUNTIME_OUTPUT_DIRECTORY
${PROJECT_BINARY_DIR}/bin)
if (STDLIB_VS)
# Disable warnings about unsecure (although standard) functions
# @see https://msdn.microsoft.com/en-us/library/aa985974.aspx
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -D_SCL_SECURE_NO_WARNINGS)
# 'strcpy' is deprecated: This function or variable may be unsafe.
# Consider using strcpy_s instead. To disable deprecation, use
# @see https://msdn.microsoft.com/en-us/library/8ef0s5kh.aspx
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -D_CRT_SECURE_NO_WARNINGS)
endif()
# Set Warnings
# NOTE(marehr): COMPILER_CLANG on windows uses the same flags as on linux,
# whereas COMPILER_WINTEL uses on windows the same flags as COMPILER_MSVC.
if (COMPILER_MSVC)
# TODO(h-2): raise this to W4
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} /W2")
elseif (COMPILER_WINTEL)
# TODO(h-2): raise this to W4
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} /W3")
else()
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -W -Wall -pedantic")
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64)
# disable some warnings on ICC
if (COMPILER_LINTEL)
# warning #3373: nonstandard use of "auto" to both deduce the type
# from an initializer and to announce a trailing return type
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -wd3373,2102")
endif ()
endif ()
if (NOT SEQAN_BUILD_SYSTEM)
set (SEQAN_BUILD_SYSTEM "DEVELOP" CACHE STRING "Build/Release mode to select. One of DEVELOP SEQAN_RELEASE, APP:\${APP_NAME}. Defaults to DEVELOP.")
endif (NOT SEQAN_BUILD_SYSTEM)
set (SEQAN_APP_VERSION "0.0.0" CACHE STRING "Version of the application.")
set (SEQAN_NIGHTLY_RELEASE FALSE CACHE BOOL "Set to TRUE to enable nightly app releases.")
## options
# SeqAn Version Check
if (SEQAN_DISABLE_VERSION_CHECK) # Disable completely
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -DSEQAN_DISABLE_VERSION_CHECK)
elseif (SEQAN_VERSION_CHECK_OPT_IN) # Build it but make it opt-in.
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -DSEQAN_VERSION_CHECK_OPT_IN)
endif ()
# Architecture.
if ((NOT SEQAN_64BIT_TARGET_PLATFORM) OR COMPILER_MSVC)
set (SEQAN_ARCH_SSE4 FALSE)
set (SEQAN_ARCH_AVX2 FALSE)
set (SEQAN_ARCH_AVX512_KNL FALSE)
set (SEQAN_ARCH_AVX512_SKX FALSE)
set (SEQAN_ARCH_AVX512_CNL FALSE)
endif ()
if (COMPILER_MSVC)
set (SEQAN_STATIC_APPS FALSE)
set (SEQAN_ARCH_NATIVE FALSE)
endif ()
if (${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD")
set (SEQAN_STATIC_APPS FALSE)
if (SEQAN_ARCH_NATIVE)
set (SEQAN_ARCH_NATIVE FALSE)
set (SEQAN_ARCH_SSE4 TRUE)
message (STATUS "OpenBSD does not support native, but SSE4 was activated instead.")
endif ()
endif ()
# Enable SSE4 if AVX[\d]+ is set. (Other parts in our build system expect it
# to be set and it is basically the synonym for 'SIMD is enabled')
if (SEQAN_ARCH_AVX2 OR SEQAN_ARCH_AVX512_KNL OR SEQAN_ARCH_AVX512_SKX OR SEQAN_ARCH_AVX512_CNL)
set (SEQAN_ARCH_SSE4 TRUE)
endif ()
if (SEQAN_STATIC_APPS)
message (STATUS "Building static apps.")
# implementation in seqan_register_apps()
endif ()
# machine specific optimizations
if (SEQAN_ARCH_NATIVE)
message (STATUS "Building binaries optimized for this specific CPU. They might not work elsewhere.")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -march=native")
if (COMPILER_LINTEL)
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -ipo -no-prec-div -fp-model fast=2 -xHOST")
endif ()
elseif (SEQAN_ARCH_SSE4)
include (SeqAnSimdUtility)
if (NOT ${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -mpopcnt")
endif ()
if (COMPILER_LINTEL)
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -ipo -no-prec-div -fp-model fast=2")
endif ()
if (SEQAN_ARCH_AVX512_CNL)
message (STATUS "Building optimized binaries up to AVX512 CNL and POPCNT.")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} ${SEQAN_SIMD_AVX512_CNL_OPTIONS}")
elseif (SEQAN_ARCH_AVX512_SKX)
message (STATUS "Building optimized binaries up to AVX512 SKX and POPCNT.")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} ${SEQAN_SIMD_AVX512_SKX_OPTIONS}")
elseif (SEQAN_ARCH_AVX512_KNL)
message (STATUS "Building optimized binaries up to AVX512 KNL and POPCNT.")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} ${SEQAN_SIMD_AVX512_KNL_OPTIONS}")
elseif (SEQAN_ARCH_AVX2)
message (STATUS "Building optimized binaries up to AVX2 and POPCNT.")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} ${SEQAN_SIMD_AVX2_OPTIONS}")
else ()
message (STATUS "Building optimized binaries up to SSE4 and POPCNT.")
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} ${SEQAN_SIMD_SSE4_OPTIONS}")
endif ()
endif ()
# TODO(h-2): for icc on windows, replace the " -" in SEQAN_CXX_FLAGS with " /"
# find out whether clang/c2 takes - or / options
# enable static linkage for seqan apps
if (SEQAN_STATIC_APPS AND (NOT CMAKE_SYSTEM_NAME MATCHES "Windows"))
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
if (APPLE)
# static build not supported on apple, but at least we can include gcc libs
if (COMPILER_GCC)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++")
endif (COMPILER_GCC)
else (APPLE)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
# make sure -rdynamic isn't added automatically
set(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS)
# make sure -fPIC isn't added automatically
set(CMAKE_SHARED_LIBRARY_CXX_FLAGS)
# For unknown reasons finding .a only seems to work for libz and
# libbzip2; cmake than proceeds to wrap these in
# -Wl,-Bstatic -lz -lbz2 -Wl,-Bdynamic
# the latter reactivates dynamic linking for the system libs
# we override this behaviour here:
set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
endif (APPLE)
endif (SEQAN_STATIC_APPS AND (NOT CMAKE_SYSTEM_NAME MATCHES "Windows"))
# strip binaries when packaging
if ((CMAKE_BUILD_TYPE STREQUAL "Release") AND
(NOT SEQAN_BUILD_SYSTEM STREQUAL "DEVELOP") AND
(NOT APPLE) AND
(COMPILER_CLANG OR COMPILER_GCC))
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -s")
endif ()
# search dependencies once, globally, if in DEVELOP
if (SEQAN_BUILD_SYSTEM STREQUAL "DEVELOP")
message (STATUS "Scanning dependencies once in DEVELOP mode...")
find_package(OpenMP)
find_package(ZLIB)
find_package(BZip2)
find_package(Boost)
find_package(SeqAn CONFIG REQUIRED)
endif ()
endmacro (seqan_build_system_init)
# ---------------------------------------------------------------------------
# Macro seqan_add_app_test (APP_NAME SUFFIX)
#
# Add app test invocation.
# ---------------------------------------------------------------------------
# App tests are run using Python. Search for Python and register test if the
# Python interpreter could be found.
macro (seqan_add_app_test APP_NAME)
if (MODEL MATCHES ".*MemCheck.*")
set (_VALGRIND_FLAG --valgrind)
else ()
set (_VALGRIND_FLAG)
endif ()
find_package (PythonInterp)
if (PYTHONINTERP_FOUND)
add_test (NAME app_test_${APP_NAME}${ARGV1}
COMMAND ${PYTHON_EXECUTABLE}
${CMAKE_CURRENT_SOURCE_DIR}/tests/run_tests${ARGV1}.py
${_VALGRIND_FLAG}
${CMAKE_SOURCE_DIR} ${CMAKE_BINARY_DIR})
endif (PYTHONINTERP_FOUND)
endmacro (seqan_add_app_test APP_NAME)
# ---------------------------------------------------------------------------
# Macro seqan_setup_library ()
#
# * Creates install targets for the library.
# * Writes list SeqAn headers to ${_SEQAN_HEADERS}
# ---------------------------------------------------------------------------
macro (seqan_setup_library)
# Only install the library if the virtual build packages "SEQAN_RELEASE"
# or "SEQAN_LIBRARY_ONLY" are chosen.
if (("${SEQAN_BUILD_SYSTEM}" STREQUAL "SEQAN_RELEASE_LIBRARY"))
# Install SeqAn LICENSE, README.rst, CHANGELOG.rst files.
install (FILES LICENSE
README.rst
CHANGELOG.rst
DESTINATION ${CMAKE_INSTALL_DOCDIR})
# Install pkg-config file, except on Windows.
if (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
configure_file("util/pkgconfig/seqan.pc.in" "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY)
install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig)
endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows)
# Install FindSeqAn TODO(h-2) rename seqan-config.cmake to seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle
install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/)
# Install headers
file (GLOB HEADERS
RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}/include/
include/seqan/[A-z]*/[A-z]/[A-z]*.h
include/seqan/[A-z]*/[A-z]*.h
include/seqan/[A-z]*.h)
foreach (HEADER ${HEADERS})
get_filename_component (_DESTINATION ${HEADER} PATH)
install (FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/${HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/${_DESTINATION})
endforeach ()
endif ()
# Get list of header and super header files.
file (GLOB SUPER_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/[A-z]*.h)
file (GLOB HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/[A-z]*/[A-z]*.h)
file (GLOB SUB_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan/[A-z]*/[A-z]*/[A-z]*.h)
# Sort headers for Xcode, ...
if (SUB_HEADERS)
list (SORT SUB_HEADERS)
endif (SUB_HEADERS)
# Sort headers for Xcode, ...
if (HEADERS)
list (SORT HEADERS)
endif (HEADERS)
# Sort super-headers for Xcode, ...
if (SUPER_HEADERS)
list (SORT SUPER_HEADERS)
endif (SUPER_HEADERS)
# Create source groups for Visual Studio (and possibly other IDEs).
foreach (HEADER ${HEADERS})
file (RELATIVE_PATH HEADER_REL ${CMAKE_CURRENT_SOURCE_DIR}/include/seqan ${HEADER})
get_filename_component (MODULE ${HEADER_REL} PATH)
source_group (seqan\\${MODULE} FILES ${HEADER})
endforeach (HEADER ${HEADERS})
source_group (seqan FILES ${SUPER_HEADERS})
# # CMake bug workaround: For Non-IDE generators there is a bug in cmake.
# # The SOURCE command in add_custom_target is not recognized there.
# set (NONIDE_GENERATORS "Unix Makefiles" "MinGW Makefiles")
# list (FIND NONIDE_GENERATORS ${CMAKE_GENERATOR} FOUND)
# if (FOUND EQUAL -1)
# set (IDE_SOURCES SOURCES ${HEADERS} ${SUPER_HEADERS})
# endif (FOUND EQUAL -1)
# Add pseudo target for the library part. Note that the IDE_SOURCES
# variable includes the "SOURCES" argument for add_custom_target when
# building with a generator for an IDE.
add_custom_target (seqan_library SOURCES ${SUB_HEADERS} ${HEADERS} ${SUPER_HEADERS})
endmacro (seqan_setup_library)
# ---------------------------------------------------------------------------
# Macro seqan_setup_install_vars (APP_NAME)
#
# Setup variables for install, depending on build mode.
# ---------------------------------------------------------------------------
macro (seqan_setup_install_vars APP_NAME)
if ("${SEQAN_BUILD_SYSTEM}" STREQUAL "APP:${APP_NAME}")
set (SEQAN_PREFIX_SHARE ".")
set (SEQAN_PREFIX_SHARE_DOC ".")
else ()
if (NOT DEFINED CMAKE_INSTALL_DOCDIR_IS_SET)
set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc" CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE)
endif ()
set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}")
set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}")
endif ()
endmacro (seqan_setup_install_vars)
# ---------------------------------------------------------------------------
# Macro seqan_install_required_system_libraries ()
#
# When packaging apps copy needed dlls
# ---------------------------------------------------------------------------
macro(INTEL_FILES_FOR_VERSION version)
# version can be 2016
set(v "${version}")
# set intel architecture
if (CMAKE_MSVC_ARCH STREQUAL "x64")
set(CMAKE_INTEL_ARCH "intel64")
else ()
set(CMAKE_INTEL_ARCH "ia32")
endif()
# Find the runtime library redistribution directory.
set(programfilesx86 "ProgramFiles(x86)")
find_path(INTEL${v}_REDIST_DIR NAMES ${CMAKE_INTEL_ARCH}/compiler
PATHS
"$ENV{ProgramFiles}/IntelSWTools/compilers_and_libraries_${v}/windows/redist"
"$ENV{${programfilesx86}}/IntelSWTools/compilers_and_libraries_${v}/windows/redist"
)
mark_as_advanced(INTEL${v}_REDIST_DIR)
set(INTEL${v}_FILES_DIR "${INTEL${v}_REDIST_DIR}/${CMAKE_INTEL_ARCH}/compiler")
if(NOT CMAKE_INSTALL_DEBUG_LIBRARIES_ONLY)
set(__install__libs
"${INTEL${v}_FILES_DIR}/libmmd.dll"
)
if(CMAKE_INSTALL_OPENMP_LIBRARIES)
set(__install__libs ${__install__libs}
"${INTEL${v}_FILES_DIR}/libiomp5md.dll"
)
endif()
else()
set(__install__libs)
endif()
if(CMAKE_INSTALL_DEBUG_LIBRARIES)
set(__install__libs ${__install__libs}
"${INTEL${v}_FILES_DIR}/libmmdd.dll"
)
endif()
foreach(lib
${__install__libs}
)
if(EXISTS ${lib})
set(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS
${CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS} ${lib})
else()
if(NOT CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS)
message(WARNING "system runtime library file does not exist: '${lib}'")
# This warning indicates an incomplete Visual Studio installation
# or a bug somewhere above here in this file.
# If you would like to avoid this warning, fix the real problem, or
# set CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS before including
# this file.
endif()
endif()
endforeach()
endmacro()
# TODO: Remove once we have cmake > 3.10.x installed on windows clients, as it should be found automatically.
macro (seqan_install_required_system_libraries)
set (CMAKE_INSTALL_OPENMP_LIBRARIES ${OPENMP_FOUND})
# include intel dll's
if(COMPILER_WINTEL)
foreach (wintel_version 2018 2017 2016)
INTEL_FILES_FOR_VERSION(wintel_version)
if (INTEL${wintel_version}_REDIST_DIR)
break()
endif ()
endforeach ()
endif()
# The following include automates the MS Redistributable installer.
set (CMAKE_INSTALL_UCRT_LIBRARIES TRUE)
include (InstallRequiredSystemLibraries)
endmacro()
# ---------------------------------------------------------------------------
# Macro seqan_configure_cpack_app (APP_NAME APP_DIR)
#
# Setup variables for install, depending on build mode.
#
# Sets defaults for CPACK_PACKAGE_DESCRIPTION_FILE and CPACK_RESOURCE_FILE_LICENSE
# ---------------------------------------------------------------------------
macro (seqan_configure_cpack_app APP_NAME APP_DIR)
seqan_install_required_system_libraries()
if (CMAKE_SYSTEM_NAME MATCHES "Windows")
set(CPACK_GENERATOR "ZIP;WIX")
file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE" license)
file(WRITE "${CMAKE_BINARY_DIR}/apps/${APP_DIR}/LICENSE.txt" "${license}")
set (CPACK_RESOURCE_FILE_LICENSE "${CMAKE_BINARY_DIR}/apps/${APP_DIR}/LICENSE.txt")
elseif (CMAKE_SYSTEM_NAME MATCHES "Darwin")
set(CPACK_GENERATOR "ZIP;DragNDrop")
elseif (CMAKE_VERSION VERSION_LESS "3.1") # TXZ support since 3.1
set(CPACK_GENERATOR "TBZ2")
else()
set(CPACK_GENERATOR "TXZ")
endif ()
if (CMAKE_SYSTEM_NAME MATCHES "Linux")
set(CPACK_GENERATOR "${CPACK_GENERATOR};DEB;RPM")
endif ()
# Set defaults for CPACK_PACKAGE_DESCRIPTION_FILE and CPACK_RESOURCE_FILE_LICENSE
if (NOT CPACK_PACKAGE_DESCRIPTION_FILE)
set (CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README")
endif ()
if (NOT CPACK_RESOURCE_FILE_LICENSE)
set (CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
endif ()
# Automatically deduce system name for CPack.
include (SetCPackSystemName)
# Get SEQAN_APP_VERSION_{MAJOR,MINOR,PATCH} from SEQAN_APP_VERSION.
set (SEQAN_APP_VERSION_MAJOR "0")
if (SEQAN_APP_VERSION MATCHES "^([0-9]+).*")
string (REGEX REPLACE "^([0-9]+).*" "\\1" _SEQAN_APP_VERSION_MAJOR "${SEQAN_APP_VERSION}")
endif ()
if (_SEQAN_APP_VERSION_MAJOR)
set(SEQAN_APP_VERSION_MAJOR "${_SEQAN_APP_VERSION_MAJOR}")
endif ()
set (SEQAN_APP_VERSION_MINOR "0")
if (SEQAN_APP_VERSION MATCHES "^[0-9]+\\.([0-9]+).*")
string (REGEX REPLACE "^[0-9]+\\.([0-9]+).*" "\\1" _SEQAN_APP_VERSION_MINOR "${SEQAN_APP_VERSION}")
endif ()
if (_SEQAN_APP_VERSION_MINOR)
set(SEQAN_APP_VERSION_MINOR "${_SEQAN_APP_VERSION_MINOR}")
endif ()
set (SEQAN_APP_VERSION_PATCH "0")
if (SEQAN_APP_VERSION MATCHES "^[0-9]+\\.[0-9]+\\.([0-9]+)$")
string (REGEX REPLACE "^[0-9]+\\.[0-9]+\\.([0-9]+)$" "\\1" _SEQAN_APP_VERSION_PATCH "${SEQAN_APP_VERSION}")
endif ()
if (_SEQAN_APP_VERSION_PATCH)
set(SEQAN_APP_VERSION_PATCH "${_SEQAN_APP_VERSION_PATCH}")
endif ()
# Setup the app version. SEQAN_APP_VERSION_{MAJOR,MINOR,PATCH} have
# to be set. To create nightly releases, set SEQAN_NIGHTLY_RELEASE to
# TRUE on the command line.
if (SEQAN_NIGHTLY_RELEASE)
include (GetCurrentDate)
set (CPACK_PACKAGE_VERSION "${CURRENT_YEAR}${CURRENT_MONTH}${CURRENT_DAY}")
else ()
set (CPACK_PACKAGE_VERSION "${SEQAN_APP_VERSION_MAJOR}.${SEQAN_APP_VERSION_MINOR}.${SEQAN_APP_VERSION_PATCH}")
endif ()
set (CPACK_PACKAGE_VERSION_MAJOR "${SEQAN_APP_VERSION_MAJOR}")
set (CPACK_PACKAGE_VERSION_MINOR "${SEQAN_APP_VERSION_MINOR}")
set (CPACK_PACKAGE_VERSION_PATCH "${SEQAN_APP_VERSION_PATCH}")
set (CPACK_PACKAGE_INSTALL_DIRECTORY "${APP_DIR} ${CPACK_PACKAGE_VERSION}")
include (CPack)
endmacro (seqan_configure_cpack_app)
# ---------------------------------------------------------------------------
# Function seqan_get_version()
#
# Sets the variables SEQAN_VERSION, SEQAN_VERSION_MAJOR, SEQAN_VERSION_MINOR,
# SEQAN_VERSION_PATCH, determined from seqan/version.h
# ---------------------------------------------------------------------------
macro (seqan_get_version)
# Read from CMAKE_SOURCE_DIR the /include/seqan/version.h
get_filename_component(_SEQAN_VERSION_H "${CMAKE_SOURCE_DIR}/include/seqan/version.h" ABSOLUTE)
# If file wasn't found seqan version is set to 0.0.0
set (_SEQAN_VERSION_IDS MAJOR MINOR PATCH PRE_RELEASE)
foreach (_ID ${_SEQAN_VERSION_IDS})
set(_SEQAN_VERSION_${_ID} "0")
endforeach(_ID ${_SEQAN_VERSION_IDS})
# Error log if version.h not found, otherwise read version from
# version.h and cache it.
if (NOT EXISTS ${_SEQAN_VERSION_H})
message ("")
message ("ERROR: Could not determine SeqAn version.")
message ("Could not find file: ${_SEQAN_VERSION_H}")
else ()
foreach (_ID ${_SEQAN_VERSION_IDS})
file (STRINGS ${_SEQAN_VERSION_H} _VERSION_${_ID} REGEX ".*SEQAN_VERSION_${_ID}.*")
string (REGEX REPLACE ".*SEQAN_VERSION_${_ID}[ |\t]+([0-9a-zA-Z]+).*" "\\1" SEQAN_VERSION_${_ID} ${_VERSION_${_ID}})
endforeach(_ID ${_SEQAN_VERSION_IDS})
endif ()
set (SEQAN_VERSION_STRING "${SEQAN_VERSION_MAJOR}.${SEQAN_VERSION_MINOR}.${SEQAN_VERSION_PATCH}")
endmacro (seqan_get_version)
# ---------------------------------------------------------------------------
# Function seqan_get_repository_info()
#
# Sets the variables SEQAN_DATE and SEQAN_REVISION determined from git.
# ---------------------------------------------------------------------------
macro (seqan_get_repository_info)
set (_SEQAN_GIT_DIR "${CMAKE_SOURCE_DIR}/.git")
message (STATUS " Selected repository dir: ${CMAKE_SOURCE_DIR}")
# Get Git information.
# But not when packaging for Debian.
# if (EXISTS ${_SEQAN_GIT_DIR})
# find_package (GitInfo QUIET)
# if (GIT_FOUND)
# GIT_WC_INFO (${CMAKE_SOURCE_DIR} _SEQAN)
# endif ()
# else ()
# message(STATUS "No revision system found.")
# endif ()
# Set SeqAn date of last commit.
if (_SEQAN_WC_LAST_CHANGED_DATE)
set (SEQAN_DATE "${_SEQAN_WC_LAST_CHANGED_DATE}")
# icc doesn't cope with spaces..
string(REPLACE " " "_" SEQAN_DATE "${SEQAN_DATE}")
message (STATUS " Determined repository date is ${SEQAN_DATE}")
else ()
message (STATUS " Repository date not determined.")
endif ()
# Set SeqAn repository revision.
if (_SEQAN_WC_REVISION)
set (SEQAN_REVISION "${_SEQAN_WC_REVISION}" CACHE INTERNAL "SeqAn repository revision.")
message (STATUS " Determined repository revision is ${SEQAN_REVISION}")
else ()
set (SEQAN_REVISION "tarball" CACHE INTERNAL "SeqAn repository revision.")
message (STATUS " Repository revision not determined.")
endif ()
endmacro (seqan_get_repository_info)
# ---------------------------------------------------------------------------
# Macro _seqan_setup_demo_test(cpp_file executable)
#
# When called with the file PATH.cpp, it will check whether PATH.cpp.stdout
# and/or PATH.cpp.stderr exists. If this is the case then we will add a test
# that runs the demo and compares the standard output/error stream with the
# given file.
#
# Used in seqan_build_demos_develop().
# ---------------------------------------------------------------------------
macro (_seqan_setup_demo_test CPP_FILE EXECUTABLE)
set (STDOUT_PATH "${CMAKE_CURRENT_SOURCE_DIR}/${CPP_FILE}.stdout")
set (STDERR_PATH "${CMAKE_CURRENT_SOURCE_DIR}/${CPP_FILE}.stderr")
if (EXISTS "${STDOUT_PATH}" OR EXISTS "${STDERR_PATH}")
# Build the path to the demo_checker.py script.
set (CHECKER_PATH "${CMAKE_SOURCE_DIR}/util/bin/demo_checker.py")
# Compose arguments to the demo_checker.py script.
if (MSVC)
# Add buildtype path and ".exe" suffix under Windows.
set (ARGS "--binary-path" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_BUILD_TYPE}/${EXECUTABLE}.exe")
elseif (WIN32)
# Add ".exe" suffix for all other Windows compilers, e.g. MinGW.
set (ARGS "--binary-path" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${EXECUTABLE}.exe")
else ()
set (ARGS "--binary-path" "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${EXECUTABLE}")
endif ()
if (EXISTS "${STDOUT_PATH}")
set (ARGS ${ARGS} "--stdout-path" "${STDOUT_PATH}")
endif ()
if (EXISTS "${STDERR_PATH}")
set (ARGS ${ARGS} "--stderr-path" "${STDERR_PATH}")
endif()
# Add the test.
find_package (PythonInterp)
if (PYTHONINTERP_FOUND)
add_test (NAME test_${EXECUTABLE}
COMMAND ${PYTHON_EXECUTABLE} ${CHECKER_PATH} ${ARGS})
#message(STATUS "add_test (NAME test_${EXECUTABLE} COMMAND ${PYTHON_EXECUTABLE} ${CHECKER_PATH} ${ARGS})")
endif (PYTHONINTERP_FOUND)
endif ()
endmacro (_seqan_setup_demo_test CPP_FILE)
# ---------------------------------------------------------------------------
# Macro seqan_register_demos([prefix])
#
# Use this in demos directories and subdirectories.
#
# This is only used when doing a Whole SeqAn Release or when developing.
# When doing a SeqAn Release then we copy over the demos, otherwise we build
# them.
# ---------------------------------------------------------------------------
function (seqan_register_demos PREFIX)
# Get a list of all .cpp and .cu files in the current directory.
file (GLOB_RECURSE ENTRIES
RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_SOURCE_DIR}/[!.]*.cpp
${CMAKE_CURRENT_SOURCE_DIR}/[!.]*.cu)
# NOTE(h-2): we do not need to search for dependencies, because this is
# done globally for DEVELOP (and demos are only built with DEVELOP)
# Supress unused parameter warnings for demos.
if (COMPILER_GCC OR COMPILER_CLANG)
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} -Wno-unused-parameter")
endif (COMPILER_GCC OR COMPILER_CLANG)
# Add SeqAn flags to CXX and NVCC flags.
# Set to PARENT_SCOPE since this macro is executed from within a function which declares it's own scope.
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}" PARENT_SCOPE)
# Setup include directories and definitions for SeqAn; flags follow below.
include_directories (${SEQAN_INCLUDE_DIRS})
# Disable version check for demos.
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -DSEQAN_DISABLE_VERSION_CHECK)
add_definitions (${SEQAN_DEFINITIONS})
# Disable the version check for all demos.
# Add all demos with found flags in SeqAn.
foreach (ENTRY ${ENTRIES})
set (SKIP FALSE)
# workaround a bug in llvm35 on FreeBSD
if ((ENTRY MATCHES "zip") AND
(${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") AND
(COMPILER_CLANG) AND
(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.5.0) AND
(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.6.0))
set (SKIP TRUE)
# bug in visual studio
elseif ((ENTRY MATCHES "queue_example.cpp") AND COMPILER_MSVC)
set (SKIP TRUE)
# all demos/* that require ZLIB[_FOUND]
elseif (NOT ZLIB_FOUND)
if ((ENTRY MATCHES "tabix_io/tabix_vcf.cpp") OR
(ENTRY MATCHES "sam_and_bam_io/example7.cpp") OR
(ENTRY MATCHES "unassigned_or_unused/bamutil.cpp"))
set (SKIP TRUE)
endif()
endif ()
if (SKIP)
message(STATUS "${ENTRY} skipped on this platform." )
else (SKIP)
string (REPLACE "/" "_" BIN_NAME "${ENTRY}")
string (REPLACE "\\" "_" BIN_NAME "${BIN_NAME}")
get_filename_component (BIN_NAME "${BIN_NAME}" NAME_WE)
get_filename_component (FILE_NAME "${ENTRY}" NAME)
add_executable(${PREFIX}${BIN_NAME} ${ENTRY})
target_link_libraries (${PREFIX}${BIN_NAME} ${SEQAN_LIBRARIES})
_seqan_setup_demo_test (${ENTRY} ${PREFIX}${BIN_NAME})
endif (SKIP)
endforeach (ENTRY ${ENTRIES})
endfunction (seqan_register_demos)
# ---------------------------------------------------------------------------
# Macro seqan_register_tests ()
# ---------------------------------------------------------------------------
# Switch to testing mode and include all subdirectories with a CMakeLists.txt
# file inside them. This function should be called in the CMakeLists.txt in
# the tests directories before including subdirectories.
#
# The following will happen:
#
# * Setting definitions SEQAN_ENABLE_DEBUG=1 and SEQAN_ENABLE_TESTING=1.
# * If the ${MODEL} variable is NightlyCoverage OR ExperimentalCoverage,
# and the compiler is GCC C++ then symbols for test coverate are added.
# * All subdirectories with a CMakeLists.txt file inside will be added.
macro (seqan_register_tests)
# Setup flags for tests.
set (SEQAN_DEFINITIONS ${SEQAN_DEFINITIONS} -DSEQAN_ENABLE_TESTING=1 -DSEQAN_DISABLE_VERSION_CHECK)
# Remove NDEBUG definition for tests.
string (REGEX REPLACE "-DNDEBUG" ""
CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO}")
string (REGEX REPLACE "-DNDEBUG" ""
CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
# Conditionally enable coverage mode by setting the appropriate flags.
if (MODEL STREQUAL "NightlyCoverage")
if (COMPILER_GCC OR COMPILER_CLANG)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
set (LDFLAGS "${LDFLAGS} -fprofile-arcs -ftest-coverage")
endif (COMPILER_GCC OR COMPILER_CLANG)
endif (MODEL STREQUAL "NightlyCoverage")
if (MODEL STREQUAL "ExperimentalCoverage")
if (COMPILER_GCC OR COMPILER_CLANG)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
set (LDFLAGS "${LDFLAGS} -fprofile-arcs -ftest-coverage")
endif (COMPILER_GCC OR COMPILER_CLANG)
endif (MODEL STREQUAL "ExperimentalCoverage")
# Add all subdirectories that have a CMakeLists.txt inside them.
file (GLOB ENTRIES
RELATIVE ${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_SOURCE_DIR}/[!.]*)
foreach (ENTRY ${ENTRIES})
if (IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY})
if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY}/CMakeLists.txt)
add_subdirectory(${ENTRY})
endif (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY}/CMakeLists.txt)
endif (IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${ENTRY})
endforeach (ENTRY ${ENTRIES})
endmacro (seqan_register_tests)
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