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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required (VERSION 2.8.12)
project (scrappie C)
option (BUILD_SHARED_LIB "Build a shared library" OFF)
set(CMAKE_CONFIGURATION_TYPES "Debug;Chaos;Release")
if(NOT CMAKE_BUILD_TYPE)
message("Defaulting to release build")
set(CMAKE_BUILD_TYPE Release)
endif()
include (InstallRequiredSystemLibraries)
set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "Scrappie is the technology demonstration platform for the Research algorithms' group.")
set (CPACK_PACKAGE_VENDOR "Oxford Nanopore Technologies")
set (CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md")
set (CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.md")
set (CPACK_PACKAGE_VERSION_MAJOR 1)
set (CPACK_PACKAGE_VERSION_MINOR 4)
set (CPACK_PACKAGE_VERSION_PATCH 0)
# Get the latest abbreviated commit hash of the working branch
execute_process(
COMMAND git log -1 --format=%h
WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
OUTPUT_VARIABLE GIT_COMMIT_HASH
OUTPUT_STRIP_TRAILING_WHITESPACE
)
set (CPACK_PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}-${GIT_COMMIT_HASH}")
set (CPACK_PACKAGE_INSTALL_DIRECTORY "CMake ${CMake_VERSION_MAJOR}.${CMake_VERSION_MINOR}")
set (CPACK_PACKAGE_NAME "ont-${PROJECT_NAME}")
set (CPACK_DEBIAN_PACKAGE_MAINTAINER "Tim Massingham <tim.massingham@nanoporetech.com>")
set (CPACK_DEBIAN_PACKAGE_SECTION "base")
set (CPACK_DEBIAN_PACKAGE_DEPENDS "libopenblas-base, libhdf5-7, libcunit1")
set (CPACK_DEBIAN_BUILD_DEPENDS "libopenblas-base, libopenblas-dev, libhdf5-7, libhdf5-dev, cmake, libcunit1-dev")
set (CPACK_PACKAGING_INSTALL_PREFIX "/opt/scrappie")
set (CPACK_GENERATOR "TGZ;DEB")
include (CPack)
configure_file (
"${PROJECT_SOURCE_DIR}/src/version.h.in"
"${PROJECT_BINARY_DIR}/include/version.h"
)
##
# Set up include directories
##
include_directories ("${PROJECT_BINARY_DIR}/include")
if (OPENBLAS_ROOT)
include_directories ("${OPENBLAS_ROOT}/include")
link_directories ("${OPENBLAS_ROOT}/lib")
set (BLAS "openblas")
else ()
set (BLAS "blas")
endif ()
if (HDF5_ROOT)
include_directories ("${HDF5_ROOT}/include")
link_directories ("${HDF5_ROOT}/lib")
set (CMAKE_REQUIRED_INCLUDES ${HDF5_ROOT}/include)
endif()
##
# Set up what is to be built
##
add_library (scrappie_objects OBJECT src/decode.c src/event_detection.c src/layers.c src/networks.c src/nnfeatures.c src/scrappie_common.c src/scrappie_matrix.c src/scrappie_seq_helpers.c src/util.c src/homopolymer.c)
set_property(TARGET scrappie_objects PROPERTY POSITION_INDEPENDENT_CODE 1)
add_library (scrappie_static STATIC $<TARGET_OBJECTS:scrappie_objects>)
set_target_properties(scrappie_static PROPERTIES OUTPUT_NAME scrappie CLEAN_DIRECT_OUTPUT 1)
add_executable (test_interface src/test_interface.c)
add_executable (scrappie src/scrappie.c src/scrappie_raw.c src/scrappie_events.c src/scrappie_mappy.c src/scrappie_seqmappy.c src/scrappie_squiggle.c src/scrappie_subcommands.c src/scrappie_help.c src/fast5_interface.c src/scrappie_event_table.c)
if (BUILD_SHARED_LIB)
if (APPLE)
message (SEND_ERROR "Building shared library on OSX not yet supported")
endif (APPLE)
add_library (scrappie_shared SHARED $<TARGET_OBJECTS:scrappie_objects>)
set_target_properties(scrappie_shared PROPERTIES OUTPUT_NAME scrappie CLEAN_DIRECT_OUTPUT 1)
install (TARGETS scrappie_shared LIBRARY DESTINATION lib)
endif (BUILD_SHARED_LIB)
#if ((CMAKE_BUILD_VERSION strequal "Chaos") AND (not defined CHAOSMONKEY))
# set(CHAOSMONEY 0.1)
#endif ((CMAKE_BUILD_VERSION strequal "Chaos") AND (not defined CHAOSMONKEY))
if (NOT DEFINED CHAOSMONKEY)
set(CHAOSMONKEY 0.1)
endif ()
##
# Check whether compiler supports openmp.
##
set (CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS} -Wall -Wno-unused-function -fstack-protector-all -fgnu89-inline -O3 -march=native -std=c99 -DUSE_SSE2 -D__USE_MISC -D_POSIX_SOURCE -DNDEBUG")
set (CMAKE_C_FLAGS_CHAOS "${CMAKE_C_FLAGS} -Wall -Wno-unused-function -fstack-protector-all -fgnu89-inline -g -march=native -std=c99 -DUSE_SSE2 -D__USE_MISC -D_POSIX_SOURCE -DNDEBUG -DCHAOSMONKEY=${CHAOSMONKEY}")
set (CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS} -Werror -Wall -Wno-cpp -DABORT_ON_NULL -Wno-unused-function -fstack-protector-all -fgnu89-inline -g -march=native -std=c99 -DUSE_SSE2 -D__USE_MISC -D_POSIX_SOURCE")
# Check for OpenMP support in compiler
include (CheckCCompilerFlag)
check_c_compiler_flag ("-fopenmp" HAS_OPENMP)
if (HAS_OPENMP)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fopenmp")
set (USE_THREADS "--threads" "1")
endif (HAS_OPENMP)
# Find right hdf5 file
include (CheckIncludeFile)
check_include_file ("hdf5.h" HDF5_STANDARD)
if (HDF5_STANDARD)
set (HDF5 "hdf5")
else (HDF5_STANDARD)
check_include_file ("hdf5/serial/hdf5.h" HDF5_SERIAL)
if (HDF5_SERIAL)
set (HDF5 "hdf5_serial")
#target_include_directories (scrappie_objects PUBLIC "/usr/include/hdf5/serial")
include_directories ("/usr/include/hdf5/serial")
#target_include_directories (scrappie PUBLIC "/usr/include/hdf5/serial")
endif (HDF5_SERIAL)
endif (HDF5_STANDARD)
target_link_libraries (scrappie scrappie_static ${BLAS} ${HDF5} m)
if (APPLE)
target_link_libraries (scrappie argp)
endif (APPLE)
install (TARGETS scrappie scrappie_static RUNTIME DESTINATION bin ARCHIVE DESTINATION lib)
enable_testing()
add_executable(scrappie_unittest src/test/scrappie_test_runner.c src/test/test_map_to_sequence.c src/test/test_scrappie_util.c src/test/scrappie_util.c src/test/test_scrappie_convolution.c src/test/test_skeleton.c src/test/test_scrappie_decoding.c src/test/test_scrappie_elu.c src/test/test_scrappie_event_detection.c src/test/test_scrappie_matrix.c src/test/test_scrappie_signal.c src/test/test_scrappie_squiggle.c src/test/test_util.c)
target_include_directories(scrappie_unittest PUBLIC "src/test" "src")
target_link_libraries(scrappie_unittest scrappie_static ${BLAS} ${HDF5} m cunit)
set (READSDIR ${PROJECT_SOURCE_DIR}/reads)
set (TESTREAD "MINICOL228_20161012_FNFAB42578_MN17976_mux_scan_HG_52221_ch271_read66_strand")
set (ENV{OPENBLAS_NUM_THREADS} 1)
add_test(NAME unittest WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/src/test/ COMMAND scrappie_unittest)
add_test(test_events_call scrappie events ${USE_THREADS} ${READSDIR})
add_test(test_raw_call scrappie raw --model raw_r94 ${USE_THREADS} ${READSDIR})
add_test(test_rawrgrgr_r94_call scrappie raw --model rgrgr_r94 ${USE_THREADS} ${READSDIR})
add_test(test_rawrgrgr_r941_call scrappie raw --model rgrgr_r941 ${USE_THREADS} ${READSDIR})
add_test(test_rawrgrgr_r10_call scrappie raw --model rgrgr_r10 ${USE_THREADS} ${READSDIR})
add_test(test_rawrnnrf_r94_call scrappie raw --model rnnrf_r94 ${USE_THREADS} ${READSDIR})
add_test(test_event_table scrappie event_table ${READSDIR}/${TESTREAD}.fast5)
add_test(test_mappy scrappie mappy ${READSDIR}/${TESTREAD}.fa ${READSDIR}/${TESTREAD}.fast5)
add_test(test_seqmappy scrappie seqmappy ${READSDIR}/${TESTREAD}.fa ${READSDIR}/${TESTREAD}.fast5)
add_test(test_squiggle_r94 scrappie squiggle --model squiggle_r94 ${READSDIR}/test_squiggles.fa)
add_test(test_squiggle_r10 scrappie squiggle --model squiggle_r10 ${READSDIR}/test_squiggles.fa)
add_test(test_licence scrappie licence)
add_test(test_licence scrappie license)
add_test(test_help scrappie help)
add_test(test_help_events scrappie help events)
add_test(test_help_event_table scrappie help event_table)
add_test(test_help_raw scrappie help raw)
add_test(test_help_squiggle scrappie help squiggle)
add_test(test_version scrappie version)
add_custom_target(test-verbose COMMAND ${CMAKE_CTEST_COMMAND} --verbose)