CMakeLists.txt

# Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved
cmake_minimum_required (VERSION 2.6)
project (ion-analysis)
set(PROJECT_DESCRIPTION "Ion Torrent Data Processing Pipeline")
enable_testing()

option(ION_DO_BACKGROUND "Build with background model" ON)
mark_as_advanced(ION_DO_BACKGROUND)

option(ION_USE_CUDA "Compile CUDA code" ON)
mark_as_advanced(ION_USE_CUDA)

option(ION_USE_SYSTEM_CUDA "Use CUDA system libraries" OFF)
mark_as_advanced(ION_USE_SYSTEM_CUDA)

option(ION_USE_SYSTEM_SAMTOOLS "Use samtools system libraries" OFF)
mark_as_advanced(ION_USE_SYSTEM_SAMTOOLS)

option(ION_USE_SYSTEM_FFTW "Use fftw system libraries" OFF)
mark_as_advanced(ION_USE_SYSTEM_FFTW)

option(ION_USE_SYSTEM_HDF5 "Use hdf5 system libraries" OFF)
mark_as_advanced(ION_USE_SYSTEM_HDF5)

option(ION_USE_SYSTEM_ARMADILLO "Use armadillo system libraries" OFF)
mark_as_advanced(ION_USE_SYSTEM_ARMADILLO)

if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
    set(ION_DO_BACKGROUND OFF CACHE BOOL "Build with background model")
endif()

include(../buildTools/cmake/CMakeLists.version.txt)
include(../buildTools/cmake/CMakeLists.compiler.txt)

#custom ExternalProject_add with timeout feature
IF (${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION} STRLESS 2.8.1)
  SET(CMAKE_MODULE_PATH
    ${CMAKE_MODULE_PATH}
    ${CMAKE_CURRENT_SOURCE_DIR}/CMake
  )
ENDIF ()
include(ExternalProject)

if(ION_USE_CUDA)
  message(STATUS "BUILD with CUDA")
  add_definitions(-DION_COMPILE_CUDA)
endif()

# Where to install - override with: -DION_INSTALL_PREFIX
set(ION_INSTALL_PREFIX "/opt/ion" CACHE PATH "Ion Install Prefix")

set(CPACK_PACKAGING_INSTALL_PREFIX ${ION_INSTALL_PREFIX})
set(CPACK_SET_DESTDIR "ON")

configure_file (
    "${PROJECT_SOURCE_DIR}/debian/postinst.in"
    "${PROJECT_BINARY_DIR}/debian/postinst" @ONLY
)
configure_file (
    "${PROJECT_SOURCE_DIR}/debian/prerm.in"
    "${PROJECT_BINARY_DIR}/debian/prerm" @ONLY
)

set (ION_TS_EXTERNAL "${PROJECT_SOURCE_DIR}/../external/")
#set (ION_TS_EXTERNAL "${CMAKE_BINARY_DIR}/external/")

if(ION_USE_CUDA)
    if (NOT ION_USE_SYSTEM_CUDA)
        set(proj_name "cudatoolkit")
#        set(proj_version "4.0.17-10.10")
        set(proj_version "4.0.0RC")
        set(proj_name_version "${proj_name}-${proj_version}")

        set(CUDA_TOOLKIT_ROOT_DIR "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/")
        set(CUDA_INCLUDE_DIRS "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/include")
        set(CUDA_NVCC_EXECUTABLE "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/bin/nvcc")
        set(CUDA_CUDART_LIBRARY "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/lib64/libcudart.so")
        set(CUDA_TOOLKIT_INCLUDE "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/include")
        set(CUDA_cublas_LIBRARY "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/lib64/libcublas.so")
        set(CUDA_cufft_LIBRARY "${ION_TS_EXTERNAL}/${proj_name_version}/src/cudatoolkit/lib64/libcufft.so")
        set(CUDA_VERBOSE_BUILD OFF)
        set(CUDA_VERSION "4.0")
        set(CUDA_64_BIT_DEVICE_CODE ON)
        include(${CMAKE_ROOT}/Modules/FindCUDA.cmake)

        # bash cudatoolkit_4.0.17_linux_64_ubuntu10.10.run --nox11 --noexec --target cudatoolkit_4.0.17_linux_64_ubuntu10.10
        # GZIP=--best tar czf cudatoolkit_4.0.17_linux_64_ubuntu10.10.tar.gz cudatoolkit_4.0.17_linux_64_ubuntu10.10/
        ExternalProject_add(${proj_name}
            PREFIX ${ION_TS_EXTERNAL}/${proj_name_version}
#            URL "http://updates.iontorrent.com/updates/software/external/cudatoolkit_4.0.17_linux_64_ubuntu10.10.tar.gz"
            URL "http://updates.iontorrent.com/updates/software/external/cudatoolkit-4.0.0RC.tar.gz"
#            URL_MD5 ""
            TIMEOUT "3600"
            CONFIGURE_COMMAND ""
            BUILD_COMMAND ""
            INSTALL_COMMAND ""
        )
    else()
        find_package(CUDA REQUIRED)
    endif()
    include_directories(${CUDA_INCLUDE_DIRS})
    message(STATUS "CUDA_LIBRARIES: ${CUDA_LIBRARIES}")
    message(STATUS "CUDA_INCLUDE_DIRS: ${CUDA_INCLUDE_DIRS}")
endif()

if (NOT ION_USE_SYSTEM_FFTW)
  set(proj_name "fftw")
  set(proj_version "3.3")
  set(proj_name_version "${proj_name}-${proj_version}")
  ExternalProject_add(${proj_name}
    PREFIX ${ION_TS_EXTERNAL}/${proj_name_version}
    URL "http://updates.iontorrent.com/updates/software/external/fftw-3.3.tar.gz"
#    URL_MD5 "0728ab3ec0ebb06631ab3b80a5c3d130"
    CONFIGURE_COMMAND ${ION_TS_EXTERNAL}/${proj_name_version}/src/${proj_name}/configure
    --enable-static --with-pic
    --prefix=${ION_TS_EXTERNAL}/${proj_name_version}
  )
  include_directories("${ION_TS_EXTERNAL}/${proj_name_version}/include")
  set(ION_FFTW_LIBS "${ION_TS_EXTERNAL}/${proj_name_version}/lib/libfftw3.a")
else()
  set(ION_FFTW_LIBS libfftw3.a)
endif()

if(NOT ION_USE_SYSTEM_HDF5)
  set(proj_name "hdf5")
  set(proj_version "1.8.8")
  set(proj_name_version "${proj_name}-${proj_version}")
  ExternalProject_add(${proj_name}
    PREFIX ${ION_TS_EXTERNAL}/${proj_name_version}
    URL "http://updates.iontorrent.com/updates/software/external/hdf5-1.8.8.tar.gz"
#    URL_MD5 1196e668f5592bfb50d1de162eb16cff
    CONFIGURE_COMMAND ${ION_TS_EXTERNAL}/${proj_name_version}/src/${proj_name}/configure
    --with-pic=yes --disable-shared --with-pthread --enable-threadsafe
    --prefix=${ION_TS_EXTERNAL}/${proj_name_version}
  )
  include_directories("${ION_TS_EXTERNAL}/${proj_name_version}/include")
  set(ION_HDF5_LIBS "${ION_TS_EXTERNAL}/${proj_name_version}/lib/libhdf5.a")
else()
  set(HDF5_USE_STATIC_LIBRARIES True)
  find_package(HDF5 REQUIRED)
  set(ION_HDF5_LIBS ${HDF5_LIBRARIES})
endif()

if(NOT ION_USE_SYSTEM_ARMADILLO)
  set(proj_name "armadillo")
  set(proj_version "1.1.0.ion0")
  set(proj_name_version "${proj_name}-${proj_version}")
  ExternalProject_add(${proj_name}_proj
    PREFIX ${ION_TS_EXTERNAL}/${proj_name_version}
    URL "http://updates.iontorrent.com/updates/software/external/armadillo-1.1.0.tar.gz"
#    URL_MD5 e8400bc7adb65fa0edc8c8ccb49b60eb
    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${ION_TS_EXTERNAL}/${proj_name_version}
    PATCH_COMMAND patch -p1 -t -N < "${PROJECT_SOURCE_DIR}/../external/armadillo-1.1.0.patch"
  )
  set(ION_ARMADILLO_LIBS "${ION_TS_EXTERNAL}/${proj_name_version}/lib64/libarmadillo.so")
  include_directories("${ION_TS_EXTERNAL}/${proj_name_version}/include")
else()
  set(ION_ARMADILLO_LIBS "armadillo")
endif()

if( 1 )
  set(proj_name "lapackpp")
  set(proj_version "2.5.4")
  set(proj_name_version "${proj_name}-${proj_version}")
  ExternalProject_add(${proj_name}
    PREFIX ${ION_TS_EXTERNAL}/${proj_name_version}
    URL "http://updates.iontorrent.com/updates/software/external/lapackpp-2.5.4.tar.gz"
#    URL_MD5 9ad74fb73fbcbf378c36a19a5dccbda7
    CONFIGURE_COMMAND ${ION_TS_EXTERNAL}/${proj_name_version}/src/${proj_name}/configure
    --enable-static --with-pic
    --prefix=${ION_TS_EXTERNAL}/${proj_name_version}
    PATCH_COMMAND patch -p1 -t -N < "${PROJECT_SOURCE_DIR}/../external/lapackpp-2.5.4.patch"
  )
  set(ION_LAPACKPP_LIBS "${ION_TS_EXTERNAL}/${proj_name_version}/lib/liblapackpp.a")
  include_directories("${ION_TS_EXTERNAL}/${proj_name_version}/include/lapackpp")
endif()

set(LIBKMEANSFILE "${PROJECT_SOURCE_DIR}/../external/kmeans-1.7/libkmeans.a")
add_custom_command(OUTPUT ${LIBKMEANSFILE}
    COMMAND "make"
    WORKING_DIRECTORY "${PROJECT_SOURCE_DIR}/../external/kmeans-1.7")
add_library(LIBKMEANS STATIC IMPORTED)
set_property(TARGET LIBKMEANS PROPERTY IMPORTED_LOCATION ${LIBKMEANSFILE})
include_directories("${PROJECT_SOURCE_DIR}/../external/kmeans-1.7")

include_directories("${PROJECT_BINARY_DIR}")
include_directories("${PROJECT_SOURCE_DIR}")
include_directories("${PROJECT_SOURCE_DIR}/../buildTools")
include_directories("${PROJECT_SOURCE_DIR}/../external/tnt-1.2.6")
include_directories("${PROJECT_SOURCE_DIR}/../external/fstrcmp")
include_directories("${PROJECT_SOURCE_DIR}/../external/jsoncpp-src-amalgated0.6.0-rc1")


if (NOT ION_USE_SYSTEM_SAMTOOLS)
  set(proj_name "samtools")
  set(proj_version "0.1.18")
  set(proj_name_version "${proj_name}-${proj_version}")
  ExternalProject_add(${proj_name}
    PREFIX ${ION_TS_EXTERNAL}/${proj_name_version}-prefix
    URL "http://updates.iontorrent.com/updates/software/external/samtools-0.1.18.tar.gz"
    #URL_MD5 7373854ca343ebee6a52874fcfc3a4a4
    # in source build
    BINARY_DIR "${ION_TS_EXTERNAL}/${proj_name_version}"
    SOURCE_DIR "${ION_TS_EXTERNAL}/${proj_name_version}"
    PATCH_COMMAND patch -p1 -t -N < "${ION_TS_EXTERNAL}/samtools-0.1.18.patch"
    CONFIGURE_COMMAND ""
    BUILD_COMMAND "/usr/bin/make" "CFLAGS=-fPIC" "<SOURCE_DIR>/Makefile" "lib"
    INSTALL_COMMAND ""
  )
  include_directories("${ION_TS_EXTERNAL}/${proj_name_version}")
  set(ION_SAMTOOLS_LIBS "${ION_TS_EXTERNAL}/${proj_name_version}/libbam.a")
else()
    set(ION_SAMTOOLS_LIBS libbam.a)
    include_directories("/usr/include/samtools")
endif()


include_directories("${PROJECT_SOURCE_DIR}/BkgModel")
include_directories("${PROJECT_SOURCE_DIR}/BaseCaller")
include_directories("${PROJECT_SOURCE_DIR}/Separator")

# CUDA Files
if(ION_USE_CUDA)
    SET( CUDA_NVCC_FLAGS "--use_fast_math" "-gencode=arch=compute_20,code=compute_20" )
    CUDA_COMPILE(CUDA_TEMP_FILES BkgModel/BkgModel.cu SHARED)
endif()

# Ion Analysis Library
add_library(ion-analysis
    ${LIBKMEANSFILE}

    ${PROJECT_BINARY_DIR}/IonVersion.cpp

    CommandLineOpts.cpp
    BarCode.cpp
    deInterlace.cpp
    
    Separator/DualGaussMixModel.cpp
    Separator/Separator.cpp
    Separator/DifferentialSeparator.cpp
    Separator/KeyClassifier.cpp
    Separator/KClass.cpp
    H5File.cpp

    SffDiffStats.cpp
    GenomeDiffStats.cpp
    FlowDiffStats.cpp
    Histogram.cpp
    Image.cpp
    IonErr.cpp
    LinuxCompat.cpp
    Mask.cpp
    RawWells.cpp
    RawWellsV1.cpp
    SFFWrapper.cpp
    Stats.cpp
    Utils.cpp
    TrackProgress.cpp
    ImageSpecClass.cpp
    ImageLoader.cpp
    SeqList.cpp
    ProcessImageToWell.cpp
    RegionTimingCalc.cpp
    WellFileManipulation.cpp
    cudaWrapper.cpp
    Zeromer.cpp
    
    OptArgs.cpp
    bivariate_gaussian.cpp
    mixed.cpp
    flow_utils.cpp
    
    BaseCaller/BaseCaller.cpp
    BaseCaller/BaseCallerLogFiles.cpp
    BaseCaller/PerBaseQual.cpp
    BaseCaller/RegionWellsReader.cpp
    BaseCaller/OrderedRegionSFFWriter.cpp
    BaseCaller/PhaseSim.cpp
    BaseCaller/PhaseSolve.cpp
    BaseCaller/PhaseFit.cpp
    BaseCaller/PhaseFitCfIe.cpp
    BaseCaller/DPTreephaser.cpp
    BaseCaller/RegionAnalysis.cpp
    BaseCaller/CafieSolver.cpp
    
    BkgModel/MathOptim.cpp
    BkgModel/MathUtil.cpp
    BkgModel/DNTPRiseModel.cpp
    BkgModel/NucStepCache.cpp
    BkgModel/DiffEqModel.cpp
    BkgModel/Hydrogen.cpp
    BkgModel/MultiFlowModel.cpp
    BkgModel/BeadParams.cpp
    BkgModel/BeadTracker.cpp
    BkgModel/RegionParams.cpp
    BkgModel/RegionTracker.cpp
    BkgModel/BeadScratch.cpp
    BkgModel/LevMarState.cpp
    BkgModel/DarkMatter.cpp
    BkgModel/DarkHalo.cpp
    BkgModel/EmphasisVector.cpp
    BkgModel/CrossTalkSpec.cpp
    BkgModel/BkgFitOptim.cpp
    BkgModel/BkgTrace.cpp
    BkgModel/SingleFlowFit.cpp
    BkgModel/BkgSearchAmplitude.cpp
    BkgModel/GlobalDefaultsForBkgModel.cpp
    BkgModel/TimeCompression.cpp
    BkgModel/Vectorization.cpp
    BkgModel/BkgFitStructures.cpp
    BkgModel/FitControl.cpp
    BkgModel/MultiLevMar.cpp
    BkgModel/BkgModel.cpp

    crop/Acq.cpp
    BFReference.cpp
    Traces.cpp

    FileEquivalent.cpp
    BubbleFilter.cpp
    ChipIdDecoder.cpp
    LSRowImageProcessor.cpp
    PinnedWellReporter.cpp
    ${PROJECT_SOURCE_DIR}/../external/fstrcmp/fstrcmp.cpp
    SamUtils/types/Cigar.cpp
    SamUtils/types/Qual.cpp
    SamUtils/types/Sequence.cpp
    SamUtils/types/BAMRead.cpp
    SamUtils/types/MD.cpp
    SamUtils/BAMReader.cpp
    SamUtils/BAMUtils.cpp
    SamUtils/alignStats.cpp

  	OptionArgsBase.cpp
  	OptionArgs.cpp
  	LoggerBase.cpp
  	Logger.cpp
	H5File.cpp
    ${PROJECT_SOURCE_DIR}/../external/jsoncpp-src-amalgated0.6.0-rc1/jsoncpp.cpp
    ${CUDA_TEMP_FILES}
)
add_dependencies(ion-analysis IONVERSION samtools fftw lapackpp armadillo_proj hdf5)
if(ION_USE_CUDA)
  if(NOT ION_USE_SYSTEM_CUDA)
    add_dependencies(ion-analysis cudatoolkit)
  endif()
endif()

target_link_libraries(ion-analysis ${ION_FFTW_LIBS} ${ION_HDF5_LIBS} LIBKMEANS ${ION_LAPACKPP_LIBS} blas lapack file-io z)
set_target_properties(ion-analysis PROPERTIES
    VERSION   "${ION_VERSION_MAJOR}.${ION_VERSION_MINOR}.${ION_VERSION_RELEASE}.${ION_VERSION_BUILDNUM}"
)
if( CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" )
        set_target_properties(ion-analysis PROPERTIES COMPILE_FLAGS "-fPIC")
endif( CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" )
install(TARGETS ion-analysis DESTINATION lib)


add_executable( SFFExtract SFFExtract.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies( SFFExtract IONVERSION TCLAP)
target_link_libraries( SFFExtract ion-analysis pthread)

add_executable( SFFExtract_sam SFFExtract_sam.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies( SFFExtract_sam IONVERSION TCLAP)
target_link_libraries( SFFExtract_sam ion-analysis pthread)

add_executable(Crop crop/Crop.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Crop IONVERSION TCLAP)
target_link_libraries(Crop ion-analysis pthread)
install(TARGETS Crop DESTINATION bin)

add_executable(Blocks crop/Blocks.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Blocks IONVERSION)
target_link_libraries(Blocks ion-analysis pthread)
install(TARGETS Blocks DESTINATION bin)

add_executable(MergeImages crop/MergeImages.cpp crop/MergeAcq.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(MergeImages IONVERSION)
target_link_libraries(MergeImages ion-analysis pthread)
install(TARGETS MergeImages DESTINATION bin)

add_executable(MergeDats crop/MergeDats.cpp crop/MergeAcq.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(MergeDats IONVERSION)
target_link_libraries(MergeDats ion-analysis pthread)
install(TARGETS MergeDats DESTINATION bin)

add_executable( GetRawAvgTraces GetRawAvgTraces.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Crop IONVERSION TCLAP)
target_link_libraries( GetRawAvgTraces ion-analysis pthread)

add_executable(Archive crop/Archive.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Archive IONVERSION TCLAP)
target_link_libraries(Archive ion-analysis pthread)

add_executable(WellsStats WellsStats.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(WellsStats IONVERSION TCLAP)
target_link_libraries(WellsStats ion-analysis pthread)

add_executable(SFFStats SFFStats.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFStats IONVERSION TCLAP)
target_link_libraries(SFFStats ion-analysis pthread)

add_executable(KeypassMetrics KeypassMetrics.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(KeypassMetrics IONVERSION TCLAP)
target_link_libraries(KeypassMetrics ion-analysis pthread)
install(TARGETS KeypassMetrics DESTINATION bin)

add_executable(HeatMaps HeatMaps.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(HeatMaps IONVERSION TCLAP)
target_link_libraries(HeatMaps ion-analysis pthread)

add_executable(GetTraces GetTraces.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(GetTraces IONVERSION TCLAP)
target_link_libraries(GetTraces ion-analysis pthread)

add_executable(Coverage Coverage.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Coverage IONVERSION TCLAP)
target_link_libraries(Coverage ion-analysis pthread)

add_executable(AsciMask2Bin AsciMask2Bin.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(AsciMask2Bin IONVERSION TCLAP)
target_link_libraries(AsciMask2Bin ion-analysis pthread)

add_executable(teMasks2Bin teMasks2Bin.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(teMasks2Bin IONVERSION TCLAP)
target_link_libraries(teMasks2Bin ion-analysis pthread)

if(ION_DO_BACKGROUND)
    add_executable(Analysis Analysis.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
    add_dependencies(Analysis IONVERSION TCLAP)

    if (ION_USE_CUDA)
        target_link_libraries(Analysis ion-analysis gsl gslcblas pthread lapack_atlas atlas ${CUDA_LIBRARIES})
    else()
        target_link_libraries(Analysis ion-analysis gsl gslcblas pthread lapack_atlas atlas)
    endif()

    install(TARGETS Analysis DESTINATION bin)

    add_executable(bkgFit bkgFit.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
    add_dependencies(bkgFit IONVERSION TCLAP)
    if (ION_USE_CUDA)
        target_link_libraries(bkgFit ion-analysis pthread ${CUDA_LIBRARIES})
    else()
        target_link_libraries(bkgFit ion-analysis pthread)
    endif()
endif()

add_executable(ShowWell ShowWell.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(ShowWell IONVERSION TCLAP)
target_link_libraries(ShowWell ion-analysis pthread)
install(TARGETS ShowWell DESTINATION bin)

add_executable(TFMapper TestFragments/TFMapper.cpp TestFragments/TFs.cpp 
    ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(TFMapper IONVERSION TCLAP)
target_link_libraries(TFMapper ion-analysis pthread)
install(TARGETS TFMapper DESTINATION bin)

add_executable(TFReferenceGenerator TestFragments/TFReferenceGenerator.cpp TestFragments/TFs.cpp
    ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(TFReferenceGenerator IONVERSION TCLAP)
target_link_libraries(TFReferenceGenerator ion-analysis pthread)
install(TARGETS TFReferenceGenerator DESTINATION bin)

add_executable(TFTorturer TestFragments/TFTorturer.cpp 
    ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(TFTorturer IONVERSION TCLAP)
target_link_libraries(TFTorturer ion-analysis ${ION_SAMTOOLS_LIBS} pthread)
install(TARGETS TFTorturer DESTINATION bin)

# add_executable(WellsTimer WellsTimer.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
# add_dependencies(WellsTimer IONVERSION TCLAP)
# target_link_libraries(WellsTimer ion-analysis pthread)
# install(TARGETS WellsTimer DESTINATION bin)

add_executable(AnalyzeHPErrs AnalyzeHPErrs.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(AnalyzeHPErrs IONVERSION TCLAP)
target_link_libraries(AnalyzeHPErrs ion-analysis pthread)

add_executable(MeasureXTalk MeasureXTalk.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(MeasureXTalk IONVERSION TCLAP)
target_link_libraries(MeasureXTalk ion-analysis pthread)

add_executable(WellCrossTalk WellCrossTalk.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(WellCrossTalk IONVERSION TCLAP)
target_link_libraries(WellCrossTalk ion-analysis pthread ${ION_ARMADILLO_LIBS})

add_executable(SFFSummary
        SFFSummary/SFFSummary.cpp
        SFFSummary/SFFSummaryDriver.cpp
        ${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(SFFSummary ion-analysis file-io pthread)
add_dependencies(SFFSummary IONVERSION TCLAP)
install(TARGETS SFFSummary DESTINATION bin)

add_executable(BeadmaskParse BeadmaskParse.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(BeadmaskParse IONVERSION TCLAP)
target_link_libraries(BeadmaskParse ion-analysis pthread)
install(TARGETS BeadmaskParse DESTINATION bin)

add_executable(BeadmaskMerge BeadmaskMerge.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(BeadmaskMerge IONVERSION TCLAP)
target_link_libraries(BeadmaskMerge ion-analysis pthread)
install(TARGETS BeadmaskMerge DESTINATION bin)

add_executable(MergeWells MergeWells.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(MergeWells IONVERSION TCLAP)
target_link_libraries(MergeWells ion-analysis pthread)
install(TARGETS MergeWells DESTINATION bin)

add_executable(Mask2TE Mask2TE.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Mask2TE IONVERSION TCLAP)
target_link_libraries(Mask2TE ion-analysis pthread)

add_executable(WellsAggregator WellsAggregator.cpp ../buildTools/dbgmem.cpp)
add_dependencies(WellsAggregator IONVERSION TCLAP)
target_link_libraries(WellsAggregator ion-analysis pthread)

add_executable(fastqsim fastqsim/fastqsim.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(fastqsim IONVERSION TCLAP)
target_link_libraries(fastqsim ion-analysis pthread)

add_executable(IonFlowAlign fastqsim/IonFlowAlign.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(IonFlowAlign IONVERSION TCLAP)
target_link_libraries(IonFlowAlign ion-analysis pthread)

include_directories("${PROJECT_SOURCE_DIR}/file-io")
add_library(file-io
        file-io/dat_chip.c
        file-io/dat_flow.c
        file-io/dat_frame.c
        file-io/dat_header.c
        file-io/dat_io.c
        file-io/fastq.c
        file-io/fastq_file.c
        file-io/ion_alloc.c
        file-io/ion_error.c
        file-io/ion_string.c
        file-io/ion_util.c
        file-io/sff.c
        file-io/sff_file.c
        file-io/sff_header.c
        file-io/sff_index.c
        file-io/sff_iter.c
        file-io/sff_read.c
        file-io/sff_read_header.c
        file-io/sff_sort.c
        file-io/wells_chip.c
        file-io/wells_data.c
        file-io/wells_header.c
        file-io/wells_mask.c
)
if( CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" )
        set_target_properties(file-io PROPERTIES COMPILE_FLAGS "-fPIC")
endif( CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" )

add_executable(phaseSolveTest
        phaseTests/phaseSolveTest.cpp
        ${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(phaseSolveTest ion-analysis file-io gsl pthread)
add_dependencies(phaseSolveTest IONVERSION TCLAP)

add_executable(SFFTrim
        SFFTrim/SFFTrim.cpp
        ${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(SFFTrim ion-analysis file-io pthread)
add_dependencies(SFFTrim IONVERSION TCLAP)
install(TARGETS SFFTrim DESTINATION bin)

add_executable(SFFSearch
        SFFTrim/SFFSearch.cpp
        ${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(SFFSearch ion-analysis file-io pthread)
add_dependencies(SFFSearch IONVERSION TCLAP)

add_executable(alignStats
        SamUtils/alignStats_driver.cpp
        ${PROJECT_BINARY_DIR}/IonVersion.cpp
)
target_link_libraries(alignStats ion-analysis z ${ION_SAMTOOLS_LIBS} pthread)
add_dependencies(alignStats IONVERSION TCLAP)
install(TARGETS alignStats DESTINATION bin)

add_executable(SFFRead fastqsim/SFFRead.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFRead IONVERSION TCLAP)
target_link_libraries(SFFRead ion-analysis pthread)
install(TARGETS SFFRead DESTINATION bin)

add_executable(SFFMerge SFFMerge.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFMerge IONVERSION)
target_link_libraries(SFFMerge ion-analysis)
install(TARGETS SFFMerge DESTINATION bin)

add_executable(SFFFilter fastqsim/SFFFilter.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFFilter IONVERSION TCLAP)
target_link_libraries(SFFFilter ion-analysis pthread)

add_executable(SFFRandom fastqsim/SFFRandom.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFRandom IONVERSION TCLAP)
target_link_libraries(SFFRandom ion-analysis pthread)
install(TARGETS SFFRandom DESTINATION bin)

add_executable(SFFAggregator fastqsim/SFFAggregate.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFAggregator IONVERSION TCLAP)
target_link_libraries(SFFAggregator ion-analysis pthread)

add_executable(Mapper fastqsim/Mapper.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(Mapper IONVERSION TCLAP)
target_link_libraries(Mapper ion-analysis pthread)

add_executable(FIXSFF fastqsim/FIXSFF.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(FIXSFF IONVERSION TCLAP)
target_link_libraries(FIXSFF ion-analysis pthread)

add_executable(SFFBT fastqsim/SFFBarcodeTrim.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFBT IONVERSION TCLAP)
target_link_libraries(SFFBT ion-analysis pthread)

add_executable(SFFPT fastqsim/SFFPrimerTrim.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFPT IONVERSION TCLAP)
target_link_libraries(SFFPT ion-analysis pthread)

add_executable(BFMaskAggregator fastqsim/BFMaskAggregate.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(BFMaskAggregator IONVERSION TCLAP)
target_link_libraries(BFMaskAggregator ion-analysis pthread)

add_executable(RawWellsEquivalent RawWellsEquivalent.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(RawWellsEquivalent IONVERSION TCLAP)
target_link_libraries(RawWellsEquivalent ion-analysis pthread)
install(TARGETS RawWellsEquivalent DESTINATION bin)

add_executable(DiffSeparator Separator/DiffSeparator.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(DiffSeparator IONVERSION TCLAP)
target_link_libraries(DiffSeparator ion-analysis pthread ${ION_ARMADILLO_LIBS})
install(TARGETS DiffSeparator DESTINATION bin)

add_executable(CountBubbles CountBubbles.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(CountBubbles IONVERSION TCLAP)
target_link_libraries(CountBubbles ion-analysis  pthread )
install(TARGETS CountBubbles DESTINATION bin)

# add_executable(RawWellsDump RawWellsDump.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
# add_dependencies(RawWellsDump IONVERSION TCLAP)
# target_link_libraries(RawWellsDump ion-analysis  pthread )
# install(TARGETS RawWellsDump DESTINATION bin)

add_executable(PinnedWell PinnedWell.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(PinnedWell IONVERSION TCLAP)
target_link_libraries(PinnedWell ion-analysis  pthread )
install(TARGETS PinnedWell DESTINATION bin)

# add_executable(LiveNeighbors LiveNeighbors.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
# add_dependencies(LiveNeighbors IONVERSION TCLAP)
# target_link_libraries(LiveNeighbors ion-analysis  pthread )
# install(TARGETS LiveNeighbors DESTINATION bin)

add_executable(readDat readDat.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(readDat IONVERSION)
target_link_libraries(readDat ion-analysis pthread)
install(TARGETS readDat DESTINATION bin)

add_executable(readWells readWells.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(readWells IONVERSION)
target_link_libraries(readWells ion-analysis pthread)
install(TARGETS readWells DESTINATION bin)

add_executable(SFFEquivalent SFFEquivalent.cpp ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFEquivalent IONVERSION TCLAP)
target_link_libraries(SFFEquivalent ion-analysis pthread)
install(TARGETS SFFEquivalent DESTINATION bin)

add_executable(iontools file-io/main.c file-io/sff_check.c ../buildTools/dbgmem.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(iontools IONVERSION TCLAP)
target_link_libraries(iontools ion-analysis file-io pthread)
install(TARGETS iontools DESTINATION bin)

add_executable(barcodeSplit barcodeSplit.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(barcodeSplit IONVERSION TCLAP)
target_link_libraries(barcodeSplit ion-analysis)
install(TARGETS barcodeSplit DESTINATION bin)

add_executable(barcodeMaskParse barcodeMaskParse.cpp ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(barcodeMaskParse IONVERSION TCLAP)
target_link_libraries(barcodeMaskParse ion-analysis)
install(TARGETS barcodeMaskParse DESTINATION bin)


add_executable(SFFUtils
  SFFUtils/SFFUtils.cpp
  SFFUtils/SFFUtilsSummary.cpp
  SFFSummary/SFFSummary.cpp
  SFFUtils/SFFUtilsRead.cpp
  ../buildTools/dbgmem.cpp
  ${PROJECT_BINARY_DIR}/IonVersion.cpp)
add_dependencies(SFFUtils IONVERSION TCLAP)
target_link_libraries(SFFUtils ion-analysis file-io pthread)
install(TARGETS SFFUtils DESTINATION bin)



# Setup for testing and gtest in particular, only needed once in file before tests.
enable_testing()
find_package(GTest QUIET)
if(GTEST_FOUND)
  
# Copy over test data...
   configure_file (
     "utest/reference.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/reference.txt"
     COPYONLY
    )
   configure_file (
     "utest/traces.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/traces.txt"
      COPYONLY
   )
   # configure_file (
   #   "utest/1.wells"
   #   "${CMAKE_CURRENT_BINARY_DIR}/1.wells"
   #    COPYONLY
   # )
   configure_file (
     "utest/reference.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/reference.txt"
     COPYONLY
   )
   configure_file (
     "utest/trimdata/sim.flow-TACG.adapter-ATCACCGACTGCCCATAGAGAGGCTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/sim.flow-TACG.adapter-ATCACCGACTGCCCATAGAGAGGCTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
     COPYONLY
    )

    configure_file (
     "utest/trimdata/sim.flow-TACG.adapter-CTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/sim.flow-TACG.adapter-CTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
      COPYONLY
     )
    configure_file (
     "utest/trimdata/sim.flow-TACGTACGTCTGAGCATCGATCGATGTACAGC.adapter-ATCACCGACTGCCCATAGAGAGGCTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/sim.flow-TACGTACGTCTGAGCATCGATCGATGTACAGC.adapter-ATCACCGACTGCCCATAGAGAGGCTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
      COPYONLY
     )
    configure_file (
     "utest/trimdata/sim.flow-TACGTACGTCTGAGCATCGATCGATGTACAGC.adapter-CTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
     "${CMAKE_CURRENT_BINARY_DIR}/sim.flow-TACGTACGTCTGAGCATCGATCGATGTACAGC.adapter-CTGAGACTGCCAAGGCACACAGGGGATAGG.txt"
      COPYONLY
     )


        include_directories(${GTEST_INCLUDE_DIRS})
        add_executable(AnalysisIntegrationTest itest/AnalysisIntegrationTest.cpp)
        target_link_libraries(AnalysisIntegrationTest ion-analysis ${GTEST_BOTH_LIBRARIES} pthread)
  # For each test file
        add_executable(PhaseFitCfIe_Test utest/PhaseFitCfIe_Test.cpp)
        target_link_libraries(PhaseFitCfIe_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(PhaseFitCfIeTest PhaseFitCfIe_Test --gtest_output=xml:./)

        add_executable(IonErr_Test utest/IonErr_Test.cpp)
        target_link_libraries(IonErr_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(IonErrTest IonErr_Test --gtest_output=xml:./)

        add_executable(Mask_Test utest/Mask_Test.cpp)
        target_link_libraries(Mask_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(MaskTest Mask_Test --gtest_output=xml:./)

        # add_executable(Wells_Test utest/Wells_Test.cpp)
        # target_link_libraries(Wells_Test ion-analysis ${ION_HDF5_LIBS} ${GTEST_BOTH_LIBRARIES} pthread z)
        # add_test(WellsTest Wells_Test --gtest_output=xml:./)

        add_executable(PhaseSim_Test utest/PhaseSim_Test.cpp)
        target_link_libraries(PhaseSim_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(PhaseSimTest PhaseSim_Test --gtest_output=xml:./)

        add_executable(PhaseSolve_Test utest/PhaseSolve_Test.cpp)
        target_link_libraries(PhaseSolve_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(PhaseSolveTest PhaseSolve_Test --gtest_output=xml:./)

        add_executable(DualGaussMixModel_Test utest/DualGaussMixModel_Test.cpp)
        target_link_libraries(DualGaussMixModel_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(DualGaussMixModelTest DualGaussMixModel_Test --gtest_output=xml:./)

        # add_executable(ZeromerDiff_Test utest/ZeromerDiff_Test.cpp)
        # target_link_libraries(ZeromerDiff_Test ion-analysis ${GTEST_BOTH_LIBRARIES}  )
        # add_test(ZeromerDiffTest ZeromerDiff_Test --gtest_output=xml:./)

        add_executable(FindSlopeChange_Test utest/FindSlopeChange_Test.cpp)
        target_link_libraries(FindSlopeChange_Test ion-analysis ${GTEST_BOTH_LIBRARIES} )
        add_test(FindSlopeChangeTest FindSlopeChange_Test --gtest_output=xml:./)

        # add_executable(KeyClassifier_Test utest/KeyClassifier_Test.cpp)
        # target_link_libraries(KeyClassifier_Test ion-analysis ${GTEST_BOTH_LIBRARIES}  )
        # add_test(KeyClassifierTest KeyClassifier_Test --gtest_output=xml:./)

        add_executable(NumericalComparison_Test utest/NumericalComparison_Test.cpp)
        target_link_libraries(NumericalComparison_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(NumericalComparisonTest NumericalComparison_Test --gtest_output=xml:./)

        add_executable(OptArgs_Test utest/OptArgs_Test.cpp)
        target_link_libraries(OptArgs_Test ion-analysis ${GTEST_BOTH_LIBRARIES} pthread)
        add_test(OptArgsTest OptArgs_Test --gtest_output=xml:./)

        add_executable(H5File_Test utest/H5File_Test.cpp)
        target_link_libraries(H5File_Test ion-analysis ${GTEST_BOTH_LIBRARIES} pthread)
        #add_test(H5FileTest H5File_Test --gtest_output=xml:./)

        add_executable(OptionArgs_Test utest/OptionArgs_Test.cpp)
        target_link_libraries(OptionArgs_Test ion-analysis ${GTEST_BOTH_LIBRARIES} pthread)
        add_test(OptionArgsTest OptionArgs_Test --gtest_output=xml:./)

        add_executable(FlowDiffStats_Test utest/FlowDiffStats_Test.cpp)
        target_link_libraries(FlowDiffStats_Test ion-analysis ${GTEST_BOTH_LIBRARIES} pthread)
        add_test(FlowDiffStatsTest FlowDiffStats_Test --gtest_output=xml:./)

        add_executable(SFFTrim_Test utest/SFFTrim_Test.cpp)
        target_link_libraries(SFFTrim_Test ion-analysis ${GTEST_BOTH_LIBRARIES})
        add_test(SFFTrimTest SFFTrim_Test --gtest_output=xml:./)
endif()

install(FILES "${PROJECT_SOURCE_DIR}/DefaultTFs.conf" DESTINATION ${ION_INSTALL_PREFIX}/config RENAME "DefaultTFs.conf.dist")
install(FILES "${PROJECT_SOURCE_DIR}/exclusionMask_314.bin" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/exclusionMask_316.bin" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/exclusionMask_318.bin" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/exclusionMask_324.bin" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/excludeMask_314" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/excludeMask_316" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/excludeMask_318" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/excludeMask_324" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/phredTable.txt_314" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/phredTable.txt_316" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/phredTable.txt_318" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/gopt_314.param" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/gopt_316.param" DESTINATION ${ION_INSTALL_PREFIX}/config)
install(FILES "${PROJECT_SOURCE_DIR}/gopt_318.param" DESTINATION ${ION_INSTALL_PREFIX}/config)
# perl modules used by plugins for json file parsing
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/common-sense-3.4.tar.gz" DESTINATION "/tmp/pModIn")
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/JSON-2.53.tar.gz" DESTINATION "/tmp/pModIn")
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/JSON-XS-2.32.tar.gz" DESTINATION "/tmp/pModIn")
# perl modules used by plugins for ???
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/Readonly-1.03.tar.gz" DESTINATION "/tmp/pModIn")
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/Carp-Assert-0.20.tar.gz" DESTINATION "/tmp/pModIn")
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/IPC-System-Simple-1.21.tar.gz" DESTINATION "/tmp/pModIn")
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/Statistics-LineFit-0.07.tar.gz" DESTINATION "/tmp/pModIn")
install(FILES "${PROJECT_SOURCE_DIR}/../external/perl/autodie-2.10.tar.gz" DESTINATION "/tmp/pModIn")

install(FILES "${PROJECT_SOURCE_DIR}/Analysis.1" DESTINATION share/man/man1)

if(NOT ION_USE_SYSTEM_ARMADILLO)
   install(FILES "${PROJECT_SOURCE_DIR}/../external/armadillo-1.1.0.ion0/lib64/libarmadillo.so.1" DESTINATION lib)
   install(FILES "${PROJECT_SOURCE_DIR}/../external/armadillo-1.1.0.ion0/lib64/libarmadillo.so.1.1.0" DESTINATION lib)
endif()

include(../buildTools/cmake/CMakeLists.cpack.txt)
#% nice to automate this
#Dependency Notes:
#
# The matePairIndividualTags plugin requires these packages:
#	emboss-data,emboss-lib,libnucleus6,libajax6
# The emboss package itself is not installed because of a filename conflict with
# /usr/bin/tmap.
set(CPACK_DEBIAN_PACKAGE_DEPENDS "libatlas3gf-base,
    libblas3gf,
    libc6,
    libgcc1,
    libgfortran3,
    liblapack3gf,
    libstdc++6,
    openjdk-6-jre,
    libgsl0ldbl,
    ion-gpu,
    emboss-data,
    emboss-lib,
    libnucleus6,
    libajax6")
set(CPACK_PACKAGE_DESCRIPTION "ion-analysis provides the command line workflow and supporting tools to process raw DAT files into SFF and fastq files.")
set(CPACK_DEBIAN_PACKAGE_CONTROL_EXTRA
    ${CMAKE_CURRENT_BINARY_DIR}/debian/postinst
    ${CMAKE_CURRENT_BINARY_DIR}/debian/prerm
)
include(CPack)