Add static build

CMakeLists.txt

@@ -3,17 +3,63 @@ cmake_minimum_required (VERSION 3.8)
 ## CUSTOMISE
 
 # Define the application name and version.
-project (RLM VERSION 1.1.0)
+project (RLM CXX)
 
-## BUILD
+# ----------------------------------------------------------------------------
+# App version
+# ----------------------------------------------------------------------------
+
+# change this after every release
+set (SEQAN_APP_VERSION_MAJOR "1")
+set (SEQAN_APP_VERSION_MINOR "2")
+set (SEQAN_APP_VERSION_PATCH "0")
+
+# don't change the following
+set (SEQAN_APP_VERSION "${SEQAN_APP_VERSION_MAJOR}.${SEQAN_APP_VERSION_MINOR}.${SEQAN_APP_VERSION_PATCH}")
+
+message (STATUS "RLM version is: ${SEQAN_APP_VERSION}")
+
+# ----------------------------------------------------------------------------
+# Make "Release" the default cmake build type
+# ----------------------------------------------------------------------------
 
-# Make Release default build type
 if (NOT CMAKE_BUILD_TYPE)
     set (CMAKE_BUILD_TYPE Release CACHE STRING
          "Choose the type of build, options are: Debug Release RelWithDebInfo"
          FORCE)
 endif ()
 
+# ----------------------------------------------------------------------------
+# Option static build
+# ----------------------------------------------------------------------------
+
+option (RLM_STATIC_BUILD "Include all libraries in the binaries." OFF)
+
+if (RLM_STATIC_BUILD)
+    add_definitions (-DRLM_STATIC_BUILD=1)
+    set(CMAKE_FIND_LIBRARY_SUFFIXES ".a")
+    # apple does not support fully static builds, but at least libgcc and libstdc++
+    if (APPLE)
+        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static-libgcc -static-libstdc++")
+        message (WARNING "WARNING: Builds on Mac are never fully static.")
+    else (APPLE)
+        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
+    endif (APPLE)
+    # on linux cmake adds -rdynamic automatically which clang can't handle in static builds
+    if (CMAKE_SYSTEM_NAME MATCHES "Linux")
+        SET(CMAKE_SHARED_LIBRARY_LINK_CXX_FLAGS "")
+    endif (CMAKE_SYSTEM_NAME MATCHES "Linux")
+endif (RLM_STATIC_BUILD)
+
+message(STATUS "The following options are selected for the build:")
+message(   "     RLM_STATIC_BUILD             ${RLM_STATIC_BUILD}")
+message(STATUS "Run 'cmake -LH' to get a comment on each option.")
+message(STATUS "Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option.")
+
+# ----------------------------------------------------------------------------
+# Build Setup
+# ----------------------------------------------------------------------------
+
 # Specify the directories where to store the built archives, libraries and executables
 set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
 set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
@@ -24,9 +70,31 @@ string (ASCII 27 Esc)
 set (FontBold "${Esc}[1m")
 set (FontReset "${Esc}[m")
 
-# Dependency: SeqAn3, sharg-parser.
+# ----------------------------------------------------------------------------
+# Dependencies
+# ----------------------------------------------------------------------------
+
 find_package (SeqAn3 QUIET REQUIRED HINTS lib/seqan3/build_system)
 find_package (sharg QUIET REQUIRED HINTS lib/sharg-parser/build_system)
+find_package (OpenMP QUIET)
+find_package (ZLIB   QUIET)
+
+message(STATUS "These dependencies were found:")
+message(   "     OPENMP       ${OPENMP_FOUND}      ${OpenMP_CXX_FLAGS}")
+message(   "     SEQAN3       ${SEQAN3_FOUND}      ${SEQAN3_VERSION_STRING}")
+message(   "     SHARG        ${SHARG_FOUND}      ${SHARG_VERSION}")
+message(   "     ZLIB         ${ZLIB_FOUND}      ${ZLIB_VERSION_STRING}")
+
+# Warn if Zlib was not found.
+if (NOT ZLIB_FOUND)
+  message (WARNING "WARNING: Zlib not found. Building RLM without support for gzipped input and output (this includes support for .bam).")
+endif (NOT ZLIB_FOUND)
+
+message(STATUS "The requirements were met.")
+
+# ----------------------------------------------------------------------------
+# Compiler specifics
+# ----------------------------------------------------------------------------
 
 # GCC12 and above: Disable warning about std::hardware_destructive_interference_size not being ABI-stable.
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
@@ -35,10 +103,92 @@ if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
     endif ()
 endif ()
 
+# ----------------------------------------------------------------------------
+# Add RLM targets
+# ----------------------------------------------------------------------------
+
 add_subdirectory (src)
 message (STATUS "${FontBold}You can run `make` to build the application.${FontReset}")
 
-## TEST
+# ----------------------------------------------------------------------------
+# Man-pages
+# ----------------------------------------------------------------------------
+
+# Umbrella man-page
+add_custom_command (OUTPUT RLM.1
+                    COMMAND RLM --export-help man > RLM.1
+                    DEPENDS RLM)
+
+add_custom_target (manual ALL DEPENDS RLM.1)
+
+# ----------------------------------------------------------------------------
+# Installation
+# ----------------------------------------------------------------------------
+
+# Adapt to system paths
+include (GNUInstallDirs)
+
+# Install RLM binaries into LIBEXECDIR
+install (TARGETS RLM
+         DESTINATION ${CMAKE_INSTALL_BINDIR})
+
+# Install non-binary files for the package to DOCDIR, usually ${PREFIX}/share/doc/RLM
+install (FILES LICENSE.md
+               README.md
+         DESTINATION ${CMAKE_INSTALL_DOCDIR})
+
+# Man pages into MANDIR, usually ${PREFIX}/share/man/man1 (or without share)
+install (FILES ${CMAKE_CURRENT_BINARY_DIR}/RLM.1
+         DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
+# ----------------------------------------------------------------------------
+# CPack Install
+# ----------------------------------------------------------------------------
+
+# Information
+set (CPACK_PACKAGE_NAME "RLM")
+set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "RLM - Read level DNA methylation analysis of bisulfite converted sequencing data.")
+set (CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
+set (CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE.md")
+set (CPACK_PACKAGE_VENDOR "Sara Hetzel <[email protected]>")
+set (CPACK_PACKAGE_CONTACT "${CPACK_PACKAGE_VENDOR}")
+set (CPACK_PACKAGE_VERSION_MAJOR "${SEQAN_APP_VERSION_MAJOR}")
+set (CPACK_PACKAGE_VERSION_MINOR "${SEQAN_APP_VERSION_MINOR}")
+set (CPACK_PACKAGE_VERSION_PATCH "${SEQAN_APP_VERSION_PATCH}")
+set (CPACK_PACKAGE_VERSION "${SEQAN_APP_VERSION}")
+set (CPACK_PACKAGE_INSTALL_DIRECTORY "${CPACK_PACKAGE_NAME} ${CPACK_PACKAGE_VERSION}")
+
+# Package format(s)
+if (CMAKE_SYSTEM_NAME MATCHES "Windows")
+    set(CPACK_GENERATOR "ZIP;NSIS")
+elseif (CMAKE_SYSTEM_NAME MATCHES "Darwin")
+    set(CPACK_GENERATOR "ZIP;DragNDrop")
+elseif (CMAKE_VERSION VERSION_LESS "3.1") # TXZ support since 3.1
+    set(CPACK_GENERATOR "TBZ2")
+else()
+    set(CPACK_GENERATOR "TXZ")
+endif ()
+
+if (CMAKE_SYSTEM_NAME MATCHES "Linux")
+    set(CPACK_GENERATOR "${CPACK_GENERATOR};DEB;RPM")
+endif ()
+
+# Package architecture
+if (CMAKE_SYSTEM_PROCESSOR STREQUAL "amd64")
+    set(CMAKE_SYSTEM_PROCESSOR "x86_64")
+    set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
+endif ()
+
+# Include architecture in package name
+if (NOT DEFINED CPACK_SYSTEM_NAME)
+  set(CPACK_SYSTEM_NAME "${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR}")
+endif (NOT DEFINED CPACK_SYSTEM_NAME)
+
+include (CPack)
+
+# ----------------------------------------------------------------------------
+# Add tests
+# ----------------------------------------------------------------------------
 
 enable_testing ()
 add_subdirectory (test EXCLUDE_FROM_ALL)