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CMakeLists.txt
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CMakeLists.txt
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################################################################################
# MindTheGap: Integrated detection and assembly of insertion variants
# A tool from the GATB (Genome Assembly Tool Box)
# Copyright (C) 2014 INRIA
# Authors: C.Lemaitre, G. Rizk
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
################################################################################
project(MindTheGap)
cmake_minimum_required(VERSION 2.6)
################################################################################
# The version number.
################################################################################
# The default version number is the latest official build
SET (gatb-tool_VERSION_MAJOR 2)
SET (gatb-tool_VERSION_MINOR 0)
SET (gatb-tool_VERSION_PATCH 2)
# But, it is possible to define another release number during a local build
IF (DEFINED MAJOR)
SET (gatb-tool_VERSION_MAJOR ${MAJOR})
ENDIF()
IF (DEFINED MINOR)
SET (gatb-tool_VERSION_MINOR ${MINOR})
ENDIF()
IF (DEFINED PATCH)
SET (gatb-tool_VERSION_PATCH ${PATCH})
ENDIF()
set (gatb-tool-version ${gatb-tool_VERSION_MAJOR}.${gatb-tool_VERSION_MINOR}.${gatb-tool_VERSION_PATCH})
# However, continuous integration has priority over local compilation
IF (DEFINED JENKINS_TAG)
SET (gatb-tool-version ${JENKINS_TAG})
ENDIF()
################################################################################
# Define cmake modules directory
################################################################################
SET (GATB_CORE_HOME ${PROJECT_SOURCE_DIR}/thirdparty/gatb-core/gatb-core)
SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}/cmake)
################################################################################
# SUPPORTED KMER SIZES
################################################################################
# One can uncomment this line and set the wanted values
#set (KSIZE_LIST "32 64 96 128 160 192 224 256")
################################################################################
# THIRD PARTIES
################################################################################
# We don't want to install some GATB-CORE artifacts
#SET (GATB_CORE_EXCLUDE_TOOLS 1)
SET (GATB_CORE_EXCLUDE_TESTS 1)
SET (GATB_CORE_EXCLUDE_EXAMPLES 1)
# GATB CORE
include (GatbCore)
################################################################################
# TOOL
################################################################################
# We also set a flag for TR1 management
if (use_new_cxx)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DUSE_NEW_CXX ")
endif()
message("-- cxx: ${CMAKE_CXX_FLAGS}")
# we get compilation definitions from the gatb-core part
add_definitions (${gatb-core-flags})
# SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra" )
SET( CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0")
# we give the headers directories from :
# - from project source
# - from GATB-CORE source
# - from dsk source
set (PROGRAM_SOURCE_DIR ${PROJECT_SOURCE_DIR}/src)
include_directories (${PROGRAM_SOURCE_DIR} ${gatb-core-includes})
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
# we define the files to be compiled
file (GLOB_RECURSE ProjectFiles src/*)
# we define the artifact to be built: the project binary
add_executable (${PROJECT_NAME} src/main.cpp ${ProjectFiles})
# we define which libraries to be linked with project binary
target_link_libraries (${PROJECT_NAME} ${gatb-core-libraries})
################################################################################
# PACKAGING
################################################################################
# We set the version number
SET (CPACK_PACKAGE_DESCRIPTION_SUMMARY "gatb-tool ${PROJECT_NAME}")
SET (CPACK_PACKAGE_VENDOR "Genscale team (INRIA)")
SET (CPACK_PACKAGE_VERSION_MAJOR "${gatb-tool_VERSION_MAJOR}")
SET (CPACK_PACKAGE_VERSION_MINOR "${gatb-tool_VERSION_MINOR}")
SET (CPACK_PACKAGE_VERSION_PATCH "${gatb-tool_VERSION_PATCH}")
SET (CPACK_PACKAGE_VERSION "${gatb-tool-version}")
# We set the kind of archive
SET (CPACK_GENERATOR "TGZ")
SET (CPACK_SOURCE_GENERATOR "TGZ")
# We ignore unwated files for the source archive
SET (CPACK_SOURCE_IGNORE_FILES
"^${PROJECT_SOURCE_DIR}/\\.git/" ;
"^${PROJECT_SOURCE_DIR}/\\.gitmodules" ;
"^${PROJECT_SOURCE_DIR}/\\.gitignore";
"^${PROJECT_SOURCE_DIR}/build/" ;
"^${GATB_CORE_HOME}/\\.cproject" ;
"^${GATB_CORE_HOME}/\\.git/" ;
"^${GATB_CORE_HOME}/\\.project" ;
"^${GATB_CORE_HOME}/\\.gitignore";
"^${GATB_CORE_HOME}/doc/design" ;
"^${GATB_CORE_HOME}/DELIVERY.md"
)
# We copy the project binary to the 'bin' directory
INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test DESTINATION .)
INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data DESTINATION .)
#INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc DESTINATION .)
INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/README.md DESTINATION .)
INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG.md DESTINATION .)
INSTALL (FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
# We include the "bin" tag into binary archive file name
set (CPACK_PACKAGE_FILE_NAME ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})
include (CPack)