MIA Initial commit

CMakeLists.txt

@@ -0,0 +1,135 @@
+# MIA - Mass Isotopolome Analyzer
+# Copyright (C) 2012-15 Daniel Weindl <[email protected]>
+#
+# 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(mia)
+
+cmake_minimum_required(VERSION 2.8)
+
+MESSAGE( STATUS "CMAKE_SYSTEM: " ${CMAKE_SYSTEM} )
+MESSAGE( STATUS "CMAKE_SYSTEM_NAME: " ${CMAKE_SYSTEM_NAME} )
+MESSAGE( STATUS "CMAKE_SYSTEM_VERSION: " ${CMAKE_SYSTEM_VERSION} )
+MESSAGE( STATUS "CMAKE_SYSTEM_PROCESSOR: " ${CMAKE_SYSTEM_PROCESSOR} )
+
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_FLAGS "-s -O3") # -O3
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules/")
+set(CMAKE_AUTOMOC TRUE)
+
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    if(POLICY CMP0020)
+        cmake_policy(SET CMP0020 NEW)
+    endif()
+endif()
+
+option(STATIC_LINKING "Link statically?" ON)
+if(STATIC_LINKING)
+    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+    set(Boost_USE_STATIC_LIBS ON)
+endif()
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
+    add_definitions(-DMIA_DEBUG_LEVEL=1)
+endif()
+
+option(MIA_WITH_METABOBASE "Use METABOBASE interface?" OFF)
+if(MIA_WITH_METABOBASE)
+    add_definitions(-DMIA_WITH_METABOBASE) # METABOBASE extension
+    set(METABOBASE_LIBRARY "$ENV{HOME}/src/mddb/build/src/libMDDB.a")
+    set(METABOBASE_INCLUDE_DIR "$ENV{HOME}/src/mddb/src/")
+    find_package(PQ REQUIRED)
+    include_directories(${METABOBASE_INCLUDE_DIR})
+endif()
+
+option(MIA_WITH_NETCDF_IMPORT "Add netCDF import?" ON)
+if(MIA_WITH_NETCDF_IMPORT)
+    add_definitions(-DMIA_WITH_NETCDF_IMPORT)
+    find_package(NetCDF REQUIRED)
+endif()
+
+# Set version
+set(VERSION_MAJOR "1")
+set(VERSION_MINOR "0")
+set(VERSION_PATCH "0")
+exec_program("bpp.sh" OUTPUT_VARIABLE  CMAKE_TWEAK_VERSION)
+exec_program("date +%Y%m%d%H%M" OUTPUT_VARIABLE  CMAKE_TWEAK_VERSION)
+set(VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}.${CMAKE_TWEAK_VERSION}")
+add_definitions(-DMIA_VERSION="${VERSION}")
+
+find_package(LabId REQUIRED)
+find_package(GSL REQUIRED)
+find_package(GCMS REQUIRED)
+#find_package(GraphViz REQUIRED)
+find_package(Boost COMPONENTS regex system filesystem REQUIRED)
+find_package(ZLIB REQUIRED)
+
+include_directories(
+ ${CMAKE_CURRENT_SOURCE_DIR}
+ ${CMAKE_CURRENT_BINARY_DIR}
+ ${POSTGRESQL_INCLUDE_DIR}
+ ${NetCDF_INCLUDE_DIR}
+ ${GCMS_INCLUDE_DIR}
+ ${GSL_INCLUDE_DIR}
+ ${LabId_INCLUDE_DIR}
+)
+
+add_subdirectory(src) # Lib
+add_subdirectory(gui) # GUI
+
+#############################
+# BEGIN CPACK configuration #
+#############################
+set(CPACK_PACKAGE_VERSION_MAJOR ${VERSION_MAJOR})
+set(CPACK_PACKAGE_VERSION_MINOR ${VERSION_MINOR})
+set(CPACK_PACKAGE_VERSION_PATCH ${VERSION_PATCH})
+set(CPACK_PACKAGE_VERSION_PATCH ${VERSION_PATCH})
+set(CPACK_PACKAGE_VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}.${CMAKE_TWEAK_VERSION}")
+set(CPACK_PACKAGE_CONTACT "Daniel WEINDL <[email protected]>")
+set(CPACK_PACKAGE_NAME "mia")
+set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}_${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}-${CMAKE_TWEAK_VERSION}_${CPACK_DEBIAN_PACKAGE_ARCHITECTURE}")
+set(CPACK_PACKAGE_EXECUTABLES "mia-gui" "MIA - Mass Isotopolome Analyzer")
+
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    set(CPACK_GENERATOR "NSIS")
+    set(CPACK_NSIS_MUI_ICON "${CMAKE_SOURCE_DIR}/gui/icons/programmIcon16x16.ico")
+    set(CPACK_NSIS_MUI_UNIICON ${CPACK_NSIS_MUI_ICON})
+    set(CPACK_NSIS_HELP_LINK "http://massisotopolomeanalyzer.lu/")
+    set(CPACK_NSIS_URL_INFO_ABOUT "http://massisotopolomeanalyzer.lu/")
+    set(CPACK_NSIS_CONTACT "[email protected]")
+    set(CPACK_NSIS_CREATE_ICONS "CreateShortCut '\$SMPROGRAMS\\\\$STARTMENU_FOLDER\\\\MIA.lnk' '\$INSTDIR\\\\bin\\\\mia-gui.exe'")
+    set(CPACK_NSIS_MUI_FINISHPAGE_RUN "mia-gui.exe")
+    install(FILES "${CMAKE_SOURCE_DIR}/doc/${CPACK_PACKAGE_NAME}-doc.pdf" DESTINATION "doc\\\\")
+    install(FILES "${CMAKE_SOURCE_DIR}/win32/msvcr100.dll" DESTINATION "bin\\\\")
+else()
+    set(CPACK_GENERATOR "DEB") # ;TGZ
+    exec_program("dpkg --print-architecture" OUTPUT_VARIABLE CPACK_DEBIAN_PACKAGE_ARCHITECTURE)
+    set(CPACK_DEBIAN_PACKAGE_DEPENDS "libc6,libpq5,libgsl0ldbl,libx11-xcb1,libxkbcommon-x11-0,libjpeg8,libpng12-0") # objdump -p gui/mia-gui | grep NEEDED
+    set(CPACK_DEBIAN_PACKAGE_SECTION "Science")
+    set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Mass Isotopolome Analyzer
+    Non-targeted stable isotope labeling analysis tool")
+    set(CPACK_DEBIAN_PACKAGE_SUGGESTS "metabolitedetector")
+    install(FILES "${CMAKE_SOURCE_DIR}/doc/${CPACK_PACKAGE_NAME}-doc.pdf" DESTINATION "share/doc/${CPACK_PACKAGE_NAME}")
+    install(FILES "${CMAKE_SOURCE_DIR}/${CPACK_PACKAGE_NAME}.xpm" DESTINATION "share/pixmaps")
+    install(FILES "${CMAKE_SOURCE_DIR}/deb/${CPACK_PACKAGE_NAME}.desktop" DESTINATION "share/applications")
+    install(FILES "${CMAKE_SOURCE_DIR}/deb/copyright" DESTINATION "share/doc/${CPACK_PACKAGE_NAME}")
+    exec_program("cd ${CMAKE_SOURCE_DIR}/deb; gzip -k9f mia-gui.1; gzip -k9f changelog;")
+    install(FILES "${CMAKE_SOURCE_DIR}/deb/mia-gui.1.gz" DESTINATION "share/man/man1/")
+    install(FILES "${CMAKE_SOURCE_DIR}/deb/libstdc++.so.6" DESTINATION "share/${CPACK_PACKAGE_NAME}")
+    install(FILES "${CMAKE_SOURCE_DIR}/deb/changelog.gz" DESTINATION "share/doc/${CPACK_PACKAGE_NAME}")
+endif()
+include(CPack)
+###########################
+# END CPACK configuration #
+###########################