v-0.0.5

cband · Oct 18, 2014 · 0e90ad9 · 0e90ad9
1 parent 73b1860
commit 0e90ad9
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,274 @@
+cmake_minimum_required (VERSION 2.8)
+
+#####
+#  Credits: A significant portion of this CMakeLists.txt is adapted from cmake
+#  instructions in Sailfish (Patro et al., https://github.com/kingsfordgroup/sailfish)
+#####
+
+project (MOJO)
+
+set (MAIN_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+set (MACHTYPE "x86_64")
+
+#set version numbers
+set(CPACK_PACKAGE_VERSION "0.0.2")
+set(CPACK_PACKAGE_VERSION_MAJOR "0")
+set(CPACK_PACKAGE_VERSION_MINOR "0")
+set(CPACK_PACKAGE_VERSION_PATCH "2")
+set(CPACK_GENERATOR "TGZ")
+set(CPACK_SOURCE_GENERATOR "TGZ")
+set(CPACK_PACKAGE_VENDOR "University of Chicago")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "MOJO - Gene fusion discovery from RNA-seq")
+set(CPACK_PACKAGE_NAME
+  "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+set(CPACK_SOURCE_PACKAGE_FILE_NAME
+  "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}-Source")
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
+## Set the standard required compile flags
+set (CMAKE_CXX_FLAGS "-fPIC -O3 -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DHAVE_CONFIG_H -Wall -std=c++11")
+
+if (APPLE)
+    # To allow ourselves to build a dynamic library, we have to tell the compiler
+    # that, yes, the symbols will be around at runtime.
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -undefined dynamic_lookup")
+    set (SHARED_LIB_EXTENSION "dylib")
+else()
+    set (SHARED_LIB_EXTENSION "so")
+endif()
+
+##
+# Compiler-specific C++11 activation.
+# http://stackoverflow.com/questions/10984442/how-to-detect-c11-support-of-a-compiler-with-cmake
+##
+if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU")
+    execute_process(
+        COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION)
+    if (NOT (GCC_VERSION VERSION_GREATER 4.8 OR GCC_VERSION VERSION_EQUAL 4.8))
+        message(FATAL_ERROR "${PROJECT_NAME} requires g++ 4.8 or higher.")
+    endif ()
+    set (BOOST_CONFIGURE_TOOLSET "")
+else ()
+    message(FATAL_ERROR "Your C++ compiler does not support C++11.")
+endif ()
+
+message(STATUS "BOOST_EXTRA_FLAGS = ${BOOST_EXTRA_FLAGS}")
+
+# Have CMake tell us what it's doing
+set (CMAKE_VERBOSE_MAKEFILE true)
+
+
+############
+# Bwa
+############
+set( BWA_BINARIES
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bwa/bwa
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bwa/xa2multi.pl
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bwa/qualfa2fq.pl
+)
+include(ExternalProject)
+message("Build system will fetch and build Bwa-0.7.10")
+message("==================================================================")
+ExternalProject_Add(bwa
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/bwa-0.7.10.tar.bz2
+        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source/bwa
+        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa
+        CONFIGURE_COMMAND ""
+        BUILD_COMMAND ${MAKE}
+        BUILD_IN_SOURCE 1
+        INSTALL_COMMAND mkdir -p ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa/ && cp ${BWA_BINARIES} ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa/
+)
+
+############
+# bowtie2
+############
+include(ExternalProject)
+message("Build system will fetch and build Bowtie2-2.2.3")
+message("==================================================================")
+set(BOWTIE2_BINARIES
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-align-l
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-align-s
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-build
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-build-l
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-build-s
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-inspect
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-inspect-l
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2/bowtie2-inspect-s
+)
+
+ExternalProject_Add(bowtie2
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/bowtie2-2.2.3-source.zip
+        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source/bowtie2
+        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bowtie2
+        CONFIGURE_COMMAND ""
+        BUILD_COMMAND ${MAKE}
+        BUILD_IN_SOURCE 1
+        INSTALL_COMMAND mkdir -p ${CMAKE_CURRENT_SOURCE_DIR}/external/bowtie2/ && cp ${BOWTIE2_BINARIES} ${CMAKE_CURRENT_SOURCE_DIR}/external/bowtie2
+)
+
+############
+# Bamtools
+############
+include(ExternalProject)
+message("Build system will fetch and build Bamtools")
+message("==================================================================")
+set( CMAKE_C_FLAGS "-Wall -g -O2")
+set(BAMTOOLS_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/external/source/bamtools)
+set(bamtools_INSTALL_DIR "${CMAKE_CURRENT_SOURCE_DIR}/external/bamtools")
+set(bamtools_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${bamtools_INSTALL_DIR})
+
+ExternalProject_Add(bamtools
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source
+        PREFIX ${BAMTOOLS_ROOT}
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/BamTools.v2.3.0.tar.gz
+        BINARY_DIR ${BAMTOOLS_ROOT}
+        INSTALL_DIR ${bamtools_INSTALL_DIR}
+        CMAKE_ARGS ${bamtools_CMAKE_ARGS}
+)
+set (BAM_SOURCE_DIR ${bamtools_INSTALL_DIR}/include/bamtools/ ${bamtools_INSTALL_DIR}/include/bamtools/api/ ${bamtools_INSTALL_DIR}/include/bamtools/shared/)
+set (BAM_LIB_DIR ${bamtools_INSTALL_DIR}/lib/bamtools/)
+set (BAM_LIBRARY ${bamtools_INSTALL_DIR}/lib/bamtools/libbamtools.${SHARED_LIB_EXTENSION})
+
+############
+# Blat
+############
+include(ExternalProject)
+message("Build system will fetch and build Blat")
+message("==================================================================")
+ExternalProject_Add(Blat
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/blatSrc35.tar.gz
+        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source/blat
+        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/blat
+        CONFIGURE_COMMAND ""
+        BUILD_COMMAND ${MAKE} MACHTYPE=${MACHTYPE}
+        BUILD_IN_SOURCE 1
+        INSTALL_COMMAND mkdir -p ${CMAKE_CURRENT_SOURCE_DIR}/external/blat/ && cp ${CMAKE_CURRENT_SOURCE_DIR}/external/source/blat/blat/blat ${CMAKE_CURRENT_SOURCE_DIR}/external/blat
+)
+
+############
+# Samtools
+############
+include(ExternalProject)
+message("Build system will fetch and build Samtools")
+message("==================================================================")
+set (SAMTOOLS_BINARY
+${CMAKE_CURRENT_SOURCE_DIR}/external/source/samtools/samtools
+)
+ExternalProject_Add(samtools
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/samtools-1.0.tar.bz2
+        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source/samtools
+        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/samtools
+        CONFIGURE_COMMAND ""
+        BUILD_COMMAND ${MAKE}
+        BUILD_IN_SOURCE 1
+        INSTALL_COMMAND mkdir -p ${CMAKE_CURRENT_SOURCE_DIR}/external/samtools/ && cp ${SAMTOOLS_BINARY} ${CMAKE_CURRENT_SOURCE_DIR}/external/samtools
+)
+
+############
+# Zlib
+############
+include(ExternalProject)
+message("Build system will fetch and build Zlib")
+message("==================================================================")
+set( CMAKE_C_FLAGS "-Wall -g -O2")
+set(ZLIB_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/external/source/zlib)
+set(zlib_INSTALL_DIR "${CMAKE_CURRENT_SOURCE_DIR}/external/zlib")
+set(zlib_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${zlib_INSTALL_DIR})
+ExternalProject_Add(ZLIB
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source
+        PREFIX ${ZLIB_ROOT}
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/zlib-1.2.8.tar.gz
+        BINARY_DIR ${ZLIB_ROOT}
+        INSTALL_DIR ${zlib_INSTALL_DIR}
+        CMAKE_ARGS ${zlib_CMAKE_ARGS}
+)
+
+
+set( BOOST_EXTRA_FLAGS "--layout=tagged" )
+
+##
+# Super-secret override
+##
+if ( DEFINED CUSTOM_BOOST_PATH )
+        set (CMAKE_INCLUDE_PATH ${CUSTOM_BOOST_PATH} ${CMAKE_INCLUDE_PATH})
+    set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
+endif ( DEFINED CUSTOM_BOOST_PATH )
+
+##
+# We want dyanmic, multithreaded boost libraries
+##
+set (Boost_USE_STATIC_LIBS OFF)
+set (Boost_USE_MULTITHREADED ON)
+set (Boost_USE_STATIC_RUNTIME OFF)
+
+set(Boost_ADDITIONAL_VERSIONS "1.55" "1.55.0")
+find_package(Boost 1.55.0 COMPONENTS regex program_options system filesystem thread log_setup log iostreams date_time timer chrono)
+
+# Download and install boost if not found 
+include(ExternalProject)
+if (NOT Boost_FOUND ) 
+    message("==================================================================")
+    message(STATUS
+	"MOJO requires Boost 1.55.0 installed. A prior installation of boost-1.55.0 is not found (BOOST_ROOT). \n"
+        "\tConfiguring to fetch and install boost \n"
+    )
+    set(BOOST_WILL_RECONFIGURE TRUE)
+    message("==================================================================")
+    ExternalProject_Add(libboost
+        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source/
+        URL http://dmel.uchicago.edu/~chai/MOJO/external/boost_1_55_0.tar.gz
+        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/source/boost_1_55_0
+        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55
+        CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/source/boost_1_55_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} --prefix=<INSTALL_DIR>
+        BUILD_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/source/boost_1_55_0/b2 ${BOOST_EXTRA_FLAGS} install
+        BUILD_IN_SOURCE 1
+        INSTALL_COMMAND ""
+    )
+
+    ExternalProject_Add_Step(libboost reconfigure
+        COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} -DBOOST_WILL_RECONFUGRE=FALSE -DBOOST_RECONFIGURE=TRUE
+        DEPENDEES install
+    )
+endif()
+
+##
+# If we're fetching boost and we need to have dummy paths for these variables
+# so that CMake won't complain
+##
+if (BOOST_WILL_RECONFIGURE)
+    message("Setting Temporary Boost paths")
+    set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55/include)
+    set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55/include)
+    set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55/lib)
+    set(Boost_FOUND TRUE)
+endif()
+
+##
+#  If we had to fetch Boost, the reconfigure step will re-run cmake.  The second configuration
+#  pass is executed with the BOOST_RECONFIGURE flag set. This should allow our newly
+#  installed Boost to be found by CMake.
+##
+if (BOOST_RECONFIGURE)
+    unset(Boost_FOUND CACHE)
+    unset(Boost_INCLUDE_DIR CACHE)
+    unset(Boost_INCLUDE_DIRS CACHE)
+    unset(Boost_LIBRARY_DIRS CACHE)
+    unset(Boost_LIBRARIES CACHE)
+    unset(BOOST_ROOT CACHE)
+    unset(CMAKE_PREFIX_PATH CACHE)
+    set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55)
+    set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55/include)
+        set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_55/lib)
+        find_package(Boost 1.55.0 COMPONENTS regex program_options system filesystem thread log_setup log iostreams date_time timer chrono)
+endif()
+
+
+add_subdirectory ( src )
+
+include (CPack)