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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required (VERSION 2.8)
enable_testing()
project (Sailfish)
set(CPACK_PACKAGE_VERSION "0.8.0")
set(CPACK_PACKAGE_VERSION_MAJOR "0")
set(CPACK_PACKAGE_VERSION_MINOR "8")
set(CPACK_PACKAGE_VERSION_PATCH "0")
set(CPACK_GENERATOR "TGZ")
set(CPACK_SOURCE_GENERATOR "TGZ")
set(CPACK_PACKAGE_VENDOR "Stony Brook University / Carnegie Mellon University")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Sailfish - Alignment-free RNA-seq isoform quantification")
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 (WARNING_IGNORE_FLAGS "-Wno-deprecated-register")
set (BOOST_CXX_FLAGS "-Wno-deprecated-register -std=c++11")
## Prefer static to dynamic libraries
SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
## Set the standard required compile flags
# Nov 18th --- removed -DHAVE_CONFIG_H
set (CMAKE_CXX_FLAGS "-pthread -funroll-loops -fPIC -fomit-frame-pointer -Ofast -DHAVE_ANSI_TERM -DHAVE_SSTREAM -DRAPMAP_SALMON_SUPPORT -Wall -std=c++11 -Wreturn-type -Werror=return-type")
##
# OSX is strange (some might say, stupid in this regard). Deal with it's quirkines here.
##
if (APPLE)
# To allow ourselves to build a dynamic library, we have to tell the compiler
# that, yes, the symbols will be around at runtime.
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -undefined dynamic_lookup")
set (LIBSAILFISH_LINKER_FLAGS "-all_load")
# In order to "think different", we also have to use non-standard suffixes
# for our shared libraries
set(SHARED_LIB_EXTENSION "dylib")
else()
# We're in sane linux world
set (SHARED_LIB_EXTENSION "so")
set (LIBSAILFISH_LINKER_FLAGS "")
endif()
set( BOOST_EXTRA_FLAGS "--layout=tagged" )
## this get's set differently below if we
## are on clang & apple
set (NON_APPLECLANG_LIBS gomp rt)
set (PTHREAD_LIB)
##
# Compiler-specific C++11 activation.
# http://stackoverflow.com/questions/10984442/how-to-detect-c11-support-of-a-compiler-with-cmake
##
##
# First take care of what to do if we have gcc
##
if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU")
execute_process(
COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION)
# If we're on OSX
if (APPLE AND NOT (GCC_VERSION VERSION_GREATER 4.8.2 OR GCC_VERSION VERSION_EQUAL 4.8.2))
message(FATAL_ERROR "When building under OSX, ${PROJECT_NAME} requires "
"either clang or g++ >= 4.8.2")
elseif (NOT (GCC_VERSION VERSION_GREATER 4.7 OR GCC_VERSION VERSION_EQUAL 4.7))
message(FATAL_ERROR "${PROJECT_NAME} requires g++ 4.7 or greater.")
endif ()
set (GCC TRUE)
# Put complete static linking on hold for the time-being
# If we're not on OSX, make an attempt to compile everything statically
#if (NOT APPLE)
#set (CMAKE_CXX_FLAGS "-static ${CMAKE_CXX_FLAGS}")
#set (CMAKE_EXE_LINK_FLAGS "-static")
set (PTHREAD_LIB "pthread")
#endif()
# If we're on Linux (i.e. not OSX) and we're using
# gcc, then set the -static-libstdc++ flag
if (NOT APPLE)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")
endif()
set (WARNING_IGNORE_FLAGS "${WARNING_IGNORE_FLAGS} -Wno-unused-local-typedefs")
set (BOOST_TOOLSET "gcc")
set (BOOST_CONFIGURE_TOOLSET "--with-toolset=gcc")
set (BCXX_FLAGS "-std=c++11")
set (BOOST_EXTRA_FLAGS toolset=gcc cxxflags=${BCXX_FLAGS})
# Tentatively, we support clang now
elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
set(CLANG TRUE)
# If we have libc++, then try and use it
include(CheckCXXCompilerFlag)
check_cxx_compiler_flag(-stdlib=libc++ HAVE_LIBCPP)
if (HAVE_LIBCPP)
message ("It appears that you're compiling with clang and that libc++ is available, so I'll use that")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
set (BOOST_TOOLSET "clang")
set (BOOST_CONFIGURE_TOOLSET "--with-toolset=clang")
set (BCXX_FLAGS "-stdlib=libc++ -DBOOST_HAS_INT128")
set (BOOST_EXTRA_FLAGS toolset=clang cxxflags=${BCXX_FLAGS} linkflags="-stdlib=libc++")
set (JELLYFISH_CXX_FLAGS "-stdlib=libc++")
# Otherwise, use libstdc++ (and make it static)
else()
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")
endif()
# There's currently a bug with clang-3.4 & Boost 1.55 -- this hack fixes it
# but we should do something better (does this break things if CPU doesn't
# have 128-bit support)?
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_HAS_INT128")
if (APPLE)
set (NON_APPLECLANG_LIBS "")
else()
set (PTHREAD_LIB "pthread")
endif()
else ()
message(FATAL_ERROR "Your C++ compiler does not support C++11.")
endif ()
## TODO: Figure out how to detect this automatically
# If the "assembler" is too old, tell TBB not to compile
# with -mrtm
if (NO_RTM)
set (TBB_CXXFLAGS "-mno-rtm")
endif()
include(ExternalProject)
##
# Update the CXX flags according to the system and compiler
##
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${WARNING_IGNORE_FLAGS}")
if (CMAKE_BUILD_TYPE MATCHES Debug)
message ("Making Debug build")
set (CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")
elseif (CMAKE_BUILD_TYPE MATCHES Release)
message ("Making Release build")
set (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS}")
else ()
message ("Making Default build type")
endif ()
##
# Record this top-level path
##
set (GAT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
# Have CMake tell us what it's doing
set (CMAKE_VERBOSE_MAKEFILE true)
##
# 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 static, multithreaded boost libraries
##
set (Boost_USE_STATIC_LIBS ON)
set (Boost_USE_MULTITHREADED ON)
#set (Boost_USE_STATIC_RUNTIME OFF)
find_package (ZLIB)
if (NOT ZLIB_FOUND)
message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
endif()
##
# Set the latest version and look for what we need
##
set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59")
find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
message("Boost_FOUND = ${Boost_FOUND}")
include(ExternalProject)
##
# 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)
message("Executing Boost Reconfiguration")
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(BOOST_ROOT ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
find_package(Boost 1.53.0 COMPONENTS filesystem system thread timer chrono program_options REQUIRED)
set(FETCH_BOOST FALSE)
endif()
##
# Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST
# option, go and grab it for them.
##
if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST))
message(FATAL_ERROR
"Sailfish cannot be compiled without Boost.\n"
"It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n"
"This build system can also download and install a local version of boost for you (this takes a lot of time).\n"
"To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE"
)
elseif(FETCH_BOOST)
## Let the rest of the build process know we're going to be fetching boost
set (BOOST_LIB_SUBSET --with-atomic --with-chrono --with-container --with-date_time --with-exception
--with-filesystem --with-graph --with-graph_parallel --with-math
--with-program_options --with-system --with-thread
--with-timer)
set (BOOST_WILL_RECONFIGURE TRUE)
set (FETCH_BOOST FALSE)
message("Build system will fetch and build Boost")
message("==================================================================")
ExternalProject_Add(libboost
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
DOWNLOAD_COMMAND curl -k -L http://fossies.org/linux/misc/boost_1_59_0.tar.gz -o boost_1_59_0.tar.gz &&
tar xzf boost_1_59_0.tar.gz
#URL http://downloads.sourceforge.net/project/boost/boost/1.57.0/boost_1_57_0.tar.gz
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
#PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR>
BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} install
BUILD_IN_SOURCE 1
INSTALL_COMMAND ""
)
##
# After we've installed boost,
##
SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE)
ExternalProject_Add_Step(libboost reconfigure
COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
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/install/include)
set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
set(Boost_FOUND TRUE)
endif()
message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}")
message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}")
message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}")
message("BOOST LIBRAREIS = ${Boost_LIBRARIES}")
set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib)
message("Build system will build libdivsufsort")
message("==================================================================")
include(ExternalProject)
ExternalProject_Add(libdivsufsort
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort.zip
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR> -DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
)
set(SUFFARRAY_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
message("Build system will fetch and build Jellyfish")
message("==================================================================")
ExternalProject_Add(libjellyfish
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.3/jellyfish-2.2.3.tar.gz -o jellyfish-2.2.3.tgz &&
rm -fr jellyfish-2.2.3 &&
tar -xzvf jellyfish-2.2.3.tgz
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.3/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
BUILD_IN_SOURCE 1
INSTALL_COMMAND make install &&
cp config.h <INSTALL_DIR>/include/jellyfish-2.2.3/jellyfish/ &&
cp config.h <INSTALL_DIR>/include/
)
find_package(TBB)
##
#
# Fetch and build Intel's Threading Building Blocks library.
#
##
if(NOT TBB_FOUND)
set(TBB_WILL_RECONFIGURE TRUE)
# Set the appropriate compiler
if (CLANG)
set(TBB_COMPILER "clang")
else()
set(TBB_COMPILER "gcc")
endif()
message("Build system will fetch and build Intel Threading Building Blocks")
message("==================================================================")
# These are useful for the custom install step we'll do later
set(TBB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss)
set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
if ("${TBB_COMPILER}" STREQUAL "gcc")
## Don't know why it's a problem yet, but if we're using
## GCC, get rid of the DO_ITT_NOTIFY flag
set(TBB_CXXFLAGS "${TBB_CXXFLAGS} -UDO_ITT_NOTIFY")
endif()
ExternalProject_Add(libtbb
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
tar -xzvf tbb_20140724oss_src.tgz
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
PATCH_COMMAND "${TBB_PATCH_STEP}"
CONFIGURE_COMMAND ""
BUILD_COMMAND make CXXFLAGS=${TBB_CXXFLAGS} lambdas=1 compiler=${TBB_COMPILER} cfg=release tbb_build_prefix=LIBS
INSTALL_COMMAND sh -c "cp ${TBB_SOURCE_DIR}/build/LIBS_release/*.${SHARED_LIB_EXTENSION}* ${TBB_INSTALL_DIR}/lib && cp -r ${TBB_SOURCE_DIR}/include/* ${TBB_INSTALL_DIR}/include"
BUILD_IN_SOURCE 1
)
SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DTBB_WILL_RECONFIGURE=FALSE -DTBB_RECONFIGURE=TRUE)
ExternalProject_Add_Step(libtbb reconfigure
COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS}
DEPENDEES install
)
endif()
##
# If we're fetching tbb, we need to have dummy paths for these variables
# so that CMake won't complain
##
if(TBB_WILL_RECONFIGURE)
set(TBB_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
set(TBB_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib)
#set(TBB_LIBRARIES tbb tbbmalloc)
set(TBB_LIBRARIES ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbb.${SHARED_LIB_EXTENSION}
${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libtbbmalloc.${SHARED_LIB_EXTENSION}
)
endif()
##
# Similar to the Boost trick above, the libtbb reconfigure should force this code
# to be run on the second configuration pass, where it should appropriately set the
# TBB_INSTALL_DIR variable.
##
if (TBB_RECONFIGURE)
unset(TBB_FOUND CACHE)
unset(TBB_INSTALL_DIR CACHE)
unset(CMAKE_PREFIX_PATH CACHE)
set(CMAKE_PREFIX_PATH ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
set(TBB_INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install)
message("TBB_INSTALL_DIR = ${TBB_INSTALL_DIR}")
find_package(TBB)
endif()
message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
message("Build system will compile libgff")
message("==================================================================")
ExternalProject_Add(libgff
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
tar -xzvf libgff.tgz &&
rm -fr libgff &&
mv libgff-1.0 libgff
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
BINARY_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff/build
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_SOURCE_DIR}/external/install
)
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
# See if we have Jemalloc
find_package(Jemalloc)
if (Jemalloc_FOUND)
message("Found Jemalloc library --- using this memory allocator")
set (FAST_MALLOC_LIB ${JEMALLOC_LIBRARIES})
set (HAVE_FAST_MALLOC TRUE)
endif()
if (NOT HAVE_FAST_MALLOC)
# See if we have Tcmalloc
find_package(Tcmalloc)
if (Tcmalloc_FOUND)
message("Fount TCMalloc library --- using this memory allocator")
set (TCMALLOC_LIB ${Tcmalloc_LIBRARIES})
set (FAST_MALLOC_LIB ${TCMALLOC_LIB})
set (HAVE_FAST_MALLOC TRUE)
endif()
endif()
if (NOT HAVE_FAST_MALLOC)
message("Build system will fetch and use JEMalloc")
message("==================================================================")
ExternalProject_Add(libjemalloc
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
tar -xzf jemalloc-3.6.0.tar.gz
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
BUILD_IN_SOURCE TRUE
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --prefix=<INSTALL_DIR>"
INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
)
set (FAST_MALLOC_LIB ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib/libjemalloc.a)
set (HAVE_FAST_MALLOC TRUE)
endif ()
##
## This depenency is for RapMap
##
message("Build system will fetch and build SparseHash")
message("==================================================================")
ExternalProject_Add(libsparsehash
DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
tar -xzf sparsehash-2.0.2.tar.gz
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
BUILD_IN_SOURCE TRUE
INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
INSTALL_COMMAND make install
)
###
#
# Done building external dependencies.
#
###
###
#
# Grab RapMap sources for quasi-mapping code --- DURING CONFIGURE TIME!
#
####
if(NOT FETCHED_RAPMAP)
exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
endif()
###
#
# Done building external dependencies.
#
###
set (CPACK_SOURCE_IGNORE_FILES
"/src/PCA.cpp"
"/src/PCAUtils.cpp"
"/build/"
"/scripts/AggregateToGeneLevel.py"
"/scripts/ExpressionTools.py"
"/scripts/GenerateExpressionFiles.sh"
"/scripts/ParseSoftFile.py"
"/scripts/PlotCorrelation.py"
"/scripts/junk"
"/scripts/sfstrace.log"
"/scripts/SFPipeline.py"
"/bin/"
"/lib/"
"/sample_data/"
"PublishREADMEToWebsite.sh"
"/external/"
"/src/obsolete/"
"/include/obsolete/"
"WebsiteHeader.txt"
"/experimental_configs/"
".git/")
message("CPACK_SOURCE_IGNORE_FILES = ${CPACK_SOURCE_IGNORE_FILES}")
# Recurse into Sailfish source directory
add_subdirectory ( src )
# build a CPack driven installer package
include (CPack)