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# ============================================================================
# Require minimal version of cmake
# ============================================================================
CMAKE_MINIMUM_REQUIRED(VERSION 2.8.5)
# ============================================================================
# Set project name and languages
# ============================================================================
PROJECT(kissplice CXX C)
# ============================================================================
# Get GNU standard installation directories (GNUInstallDirs module)
# ============================================================================
INCLUDE(GNUInstallDirs)
# ============================================================================
# Set compilation flags
# ============================================================================
IF(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE Distribution)
ENDIF(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
SET(CMAKE_CXX_FLAGS_DEBUG "-g -Wall")
SET(CMAKE_C_FLAGS_DEBUG "-g -Wall")
SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -Wall")
SET(CMAKE_C_FLAGS_RELEASE "-O3 -Wall")
SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O3 -w")
SET(CMAKE_C_FLAGS_DISTRIBUTION "-O3 -w")
SET(CMAKE_CXX_FLAGS_PROFILING "-g -pg")
SET(CMAKE_C_FLAGS_PROFILING "-g -pg")
# ============================================================================
# Manage the KMERS_OVER_32 option
# The default value for KMERS_OVER_32 is
# * ON on 64 bits systems
# * OFF on 32 bits systems
# If a user tries to set KMERS_OVER_32 to ON on a 32 bits system, it will be
# forced back to OFF in the CACHE and a FATAL_ERROR message will be issued.
# ============================================================================
SET(KMERS_OVER_32_HELP_STRING "Increase the maximum k-mer size on 64-bits systems")
IF (${CMAKE_SIZEOF_VOID_P} LESS 8 )
set(KMERS_OVER_32 OFF CACHE BOOL KMERS_OVER_32_HELP_STRING)
IF (KMERS_OVER_32)
set(KMERS_OVER_32 OFF CACHE BOOL KMERS_OVER_32_HELP_STRING FORCE)
MESSAGE(FATAL_ERROR
"The KMERS_OVER_32 option cannot be used on 32 bits systems")
ENDIF ()
ELSE ()
set(KMERS_OVER_32 ON CACHE BOOL KMERS_OVER_32_HELP_STRING)
ENDIF ()
# ============================================================================
# Tell cmake where to put binary files.
# By GNU standards "executable programs that users can run" should go in
# bindir a.k.a ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}
# and "executable programs to be run by other programs rather than by users"
# in libexecdir a.k.a ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBEXECDIR}
#
# The main script of kissplice (kissplice.py) must be configured to find the
# secondary binaries. These can be found either in libexecdir (after install)
# or in the build-tree, we hence need 2 versions of kissplice: one that uses
# those secondary binaries in the build-tree and one that is installable.
# The latter will be placed in an ad-hoc directory called "install" in the
# build-tree
#
# Since all the files to be *compiled* belong to libexecdir, we can set
# ${CMAKE_RUNTIME_OUTPUT_DIRECTORY} once and for all her
# ============================================================================
# Set main binary dir
SET(MAIN_BIN_DIR ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
# Set the location of other executables
SET(SEC_BIN_DIR ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBEXECDIR}/kissplice)
# Tell cmake where to put compiled files
SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${SEC_BIN_DIR})
# Make a configured copy of kissplice main (python) file
# KS_SEC_EXEC_PATH must be a relative path to support local installations using
# make install DESTDIR=/some/path
set(KS_SEC_EXEC_PATH ${CMAKE_INSTALL_LIBEXECDIR}/kissplice)
configure_file(${PROJECT_SOURCE_DIR}/kissplice.py ${MAIN_BIN_DIR}/kissplice @ONLY)
# Tell cmake where to install the main script (kissplice)
install(PROGRAMS ${MAIN_BIN_DIR}/kissplice
DESTINATION ${CMAKE_INSTALL_FULL_BINDIR})
# ============================================================================
# zlib required for kissreads
# ============================================================================
FIND_PACKAGE(ZLIB REQUIRED)
# ============================================================================
# Tell cmake about subdirectories to look into
# ============================================================================
ADD_SUBDIRECTORY(debruijn-v4)
ADD_SUBDIRECTORY(thirdparty)
ADD_SUBDIRECTORY(modules)
ADD_SUBDIRECTORY(man)
ADD_SUBDIRECTORY(doc)
# ============================================================================
# Add testing capabilities
# ============================================================================
ENABLE_TESTING()
ADD_SUBDIRECTORY(tests)
# ============================================================================
# Adds the 'dist' target (that will use cpack)
# ============================================================================
add_custom_target(dist COMMAND ${CMAKE_BUILD_TOOL} package_source)
# ============================================================================
# Add custom uninstall target
# ============================================================================
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/utils/cmake/cmake_uninstall.cmake.in"
"${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
IMMEDIATE @ONLY)
add_custom_target(uninstall
COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
# ============================================================================
# Configure cpack
# ============================================================================
SET(CPACK_PACKAGE_NAME "kissplice")
SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
SET(CPACK_PACKAGE_VERSION_PATCH "0-p1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL")
SET(CPACK_SOURCE_GENERATOR "TGZ")
SET(CPACK_SOURCE_IGNORE_FILES
"README.CMake"
"README.Licence"
"README.Release"
"README.NamingConventions"
"README.Kissreads"
"CMakeFiles"
"Makefile"
"_CPack_Packages"
"CMakeCache.txt"
".*\\\\.svn"
".*\\\\.idea"
".*\\\\.DS_Store"
".*\\\\.gz"
".*\\\\~"
".*\\\\.o"
"bcc/"
"debruijn/"
"debruijn-v2"
"datasets"
"ismb"
"Recomb"
"RR"
"script_tarjan_aphid.sh"
"splice_sites_results"
"splicing_events"
"TODO.*"
"Validation"
"validation_script.sh"
".*project"
"/\\\\.git*"
"results"
"build"
"incremental-bicon.ps"
"scripts"
"skeletons"
"doc/dev"
"alt_splicing_sample_ex.png"
"quantifModel-big.png"
"resType0.png"
"resType1.png"
"quantifModel.png"
"ucsc.png"
"user_guide.aux"
"user_guide.bib"
"user_guide.log"
"user_guide.toc"
"user_guide.tex"
"jobim13"
${CPACK_SOURCE_IGNORE_FILES}
)
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
include(CPack)
|
