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Thu, May 2, 21:26
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R8820 scATAC-seq
CMakeLists.txt
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# compiler options
add_compile_options(-std=c++14)
add_compile_options(-O3)
add_compile_options(-Wall)
add_compile_options(-Wextra)
add_compile_options(-Werror)
add_compile_options(-Wfatal-errors)
add_compile_options(-pedantic)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
add_definitions (${SEQAN_DEFINITIONS})
# include file location
include_directories(${Boost_INCLUDE_DIRS})
include_directories(${SEQAN_INCLUDE_DIRS})
include_directories("${scATACseq_SOURCE_DIR}/src/Matrix")
include_directories("${scATACseq_SOURCE_DIR}/src/Clustering")
include_directories("${scATACseq_SOURCE_DIR}/src/Random")
include_directories("${scATACseq_SOURCE_DIR}/src/Parallel")
include_directories("${scATACseq_SOURCE_DIR}/src/Statistics")
include_directories("${scATACseq_SOURCE_DIR}/src/GUI")
include_directories("${scATACseq_SOURCE_DIR}/src/Applications")
include_directories("${scATACseq_SOURCE_DIR}/src/Matrix")
include_directories("${scATACseq_SOURCE_DIR}/src/GenomicTools")
include_directories("${scATACseq_SOURCE_DIR}/src/Utility")
# compile modules into static libraries
## set output directory
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/lib")
## build instructions
add_library(Clustering "Clustering/DataLayer.cpp"
"Clustering/ReadLayer.cpp"
"Clustering/SequenceLayer.cpp"
"Clustering/ModelComputer.cpp"
"Clustering/ReadModelComputer.cpp"
"Clustering/SequenceModelComputer.cpp"
"Clustering/EMBase.cpp"
"Clustering/EMRead.cpp"
"Clustering/EMSequence.cpp"
"Clustering/EMJoint.cpp")
add_library(Random "Random/Random.cpp"
"Random/RandomNumberGenerator.cpp")
add_library(Parallel "Parallel/ThreadPool.cpp")
add_library(Statistics "Statistics/Statistics.cpp")
add_library(GUI "GUI/ConsoleProgressBar.cpp"
"GUI/Diplayable.cpp"
"GUI/Updatable.cpp")
add_library(GenomicTools "GenomicTools/MatrixCreator.cpp"
"GenomicTools/ReadMatrixCreator.cpp"
"GenomicTools/CorrelationMatrixCreator.cpp"
"GenomicTools/SequenceMatrixCreator.cpp"
"GenomicTools/GenomeRegion.cpp")
add_library(Utility "Utility/matrices.cpp"
"Utility/dna_utility.cpp")
## resolve dependencies
target_link_libraries(Utility ${SEQAN_LIBRARIES})
target_link_libraries(Clustering Utility Random Statistics GUI Parallel ${SEQAN_LIBRARIES})
target_link_libraries(Parallel Threads::Threads)
target_link_libraries(GenomicTools Utility ${SEQAN_LIBRARIES})
# executables
## a toy for seqan
set(EXE_MAIN_TEST "main_test")
add_executable(${EXE_MAIN_TEST} "main_test.cpp")
target_link_libraries(${EXE_MAIN_TEST} GenomicTools Clustering)
set_target_properties(${EXE_MAIN_TEST} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## a toy for correlation matrix
set(EXE_MAIN_CORMAT "main_cormat")
add_executable(${EXE_MAIN_CORMAT} "main_cormat.cpp")
target_link_libraries(${EXE_MAIN_CORMAT} ${SEQAN_LIBRARIES} Utility GenomicTools Random)
set_target_properties(${EXE_MAIN_CORMAT} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an application to create a matrix from BED and a BAM file
set(EXE_MAIN_BAMMATRIX "CorrelationMatrixCreator")
add_executable(${EXE_MAIN_BAMMATRIX} "Applications/CorrelationMatrixCreatorApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_MAIN_BAMMATRIX} GenomicTools Utility Boost::program_options)
set_target_properties(${EXE_MAIN_BAMMATRIX} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an application to create a sequence matrix from BED and a fasta file
set(EXE_MAIN_SEQMATRIX "SequenceMatrixCreator")
add_executable(${EXE_MAIN_SEQMATRIX} "Applications/SequenceMatrixCreatorApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_MAIN_SEQMATRIX} GenomicTools Utility Boost::program_options)
set_target_properties(${EXE_MAIN_SEQMATRIX} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an EMRead standalone
set(EXE_EMREAD "EMRead")
add_executable(${EXE_EMREAD} "Applications/EMReadApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_EMREAD} Clustering Utility Boost::program_options)
set_target_properties(${EXE_EMREAD} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an EMSequence standalone
set(EXE_EMSEQ "EMSequence")
add_executable(${EXE_EMSEQ} "Applications/EMSequenceApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_EMSEQ} Clustering Utility Boost::program_options)
set_target_properties(${EXE_EMSEQ} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an EMJoint standalone
set(EXE_EMJOINT "EMJoint")
add_executable(${EXE_EMJOINT} "Applications/EMJointApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_EMJOINT} Clustering Utility Boost::program_options)
set_target_properties(${EXE_EMJOINT} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an executable to compute data models from the data and the post prob of an EM classification
set(EXE_PROB2REF "ProbToModel")
add_executable(${EXE_PROB2REF} "Applications/ProbToModelApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_PROB2REF} Clustering Utility Boost::program_options)
set_target_properties(${EXE_PROB2REF} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an executable to extend read models from an EM classification
set(EXE_READMODELEXTENDER "ReadModelExtender")
add_executable(${EXE_READMODELEXTENDER} "Applications/ReadModelExtenderApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_READMODELEXTENDER} Clustering GenomicTools Utility Boost::program_options)
set_target_properties(${EXE_READMODELEXTENDER} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an executable to extend read models from an EM classification
set(EXE_SEQUENCEMODELEXTENDER "SequenceModelExtender")
add_executable(${EXE_SEQUENCEMODELEXTENDER} "Applications/SequenceModelExtenderApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_SEQUENCEMODELEXTENDER} Clustering GenomicTools Utility Boost::program_options)
set_target_properties(${EXE_SEQUENCEMODELEXTENDER} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## a test suite
set(EXE_TESTS "unittests")
add_executable(${EXE_TESTS} "unittests.cpp"
"Unittests/unittests_matrix.cpp"
"Unittests/unittests_genomictools.cpp")
target_link_libraries(${EXE_TESTS} ${UNITTEST_LIB} ${SEQAN_LIBRARIES} GenomicTools)
set_target_properties(${EXE_TESTS} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
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