Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F62809861
CMakeLists.txt
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, May 15, 19:49
Size
9 KB
Mime Type
text/x-Algol68
Expires
Fri, May 17, 19:49 (2 d)
Engine
blob
Format
Raw Data
Handle
17692134
Attached To
R8820 scATAC-seq
CMakeLists.txt
View Options
# 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/Data2DLayer.cpp"
"Clustering/Data3DLayer.cpp"
"Clustering/ReadLayer.cpp"
"Clustering/SequenceLayer.cpp"
"Clustering/ConsensusSequenceLayer.cpp"
"Clustering/ModelComputer.cpp"
"Clustering/ReadModelComputer.cpp"
"Clustering/SequenceModelComputer.cpp"
"Clustering/ConsensusSequenceModelComputer.cpp"
"Clustering/EMBase.cpp"
"Clustering/EMRead.cpp"
"Clustering/EMSequence.cpp"
"Clustering/EMConsensusSequence.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"
"Statistics/KmersStatistics.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/ClassReadDataCreator.cpp"
"GenomicTools/ClassSequenceDataCreator.cpp"
"GenomicTools/SequenceMatrixCreator.cpp"
"GenomicTools/GenomeRegion.cpp")
add_library(Utility "Utility/matrix_utility.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 "${scATACseq_SOURCE_DIR}/bin")
## an application to read binary matrices and display them in txt
set(EXE_MAIN_MATBIN2TXT "MatrixBinToTxt")
add_executable(${EXE_MAIN_MATBIN2TXT} "Applications/MatrixBinToTxtApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_MAIN_MATBIN2TXT} Utility Boost::program_options)
set_target_properties(${EXE_MAIN_MATBIN2TXT} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an application to know the indices of 0-signal rows in integer 2D matrices
set(EXE_MAIN_WHICHNULLROWS "WhichNullRows")
add_executable(${EXE_MAIN_WHICHNULLROWS} "Applications/WhichNullRowsApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_MAIN_WHICHNULLROWS} Boost::program_options)
set_target_properties(${EXE_MAIN_WHICHNULLROWS} 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(${EXE_EMREAD} Clustering Boost::program_options)
set_target_properties(${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 "${scATACseq_SOURCE_DIR}/bin")
## an EMConsensusSequence standalone
set(EXE_EMCONSSEQ "EMConsensusSequence")
add_executable(${EXE_EMCONSSEQ} "Applications/EMConsensusSequenceApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_EMCONSSEQ} Clustering Utility Boost::program_options)
set_target_properties(${EXE_EMCONSSEQ} 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 "${scATACseq_SOURCE_DIR}/bin")
## an executable to extract read data from an EM classification
set(EXE_CLASSREADDATACREATOR "ClassReadDataCreator")
add_executable(${EXE_CLASSREADDATACREATOR} "Applications/ClassReadDataCreatorApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_CLASSREADDATACREATOR} Clustering GenomicTools Utility Boost::program_options)
set_target_properties(${EXE_CLASSREADDATACREATOR} PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${scATACseq_SOURCE_DIR}/bin")
## an executable to extract sequence data from an EM classification
set(EXE_CLASSSEQDATACREATOR "ClassSequenceDataCreator")
add_executable(${EXE_CLASSSEQDATACREATOR} "Applications/ClassSequenceDataCreatorApplication.cpp" "Applications/ApplicationInterface.cpp")
target_link_libraries(${EXE_CLASSSEQDATACREATOR} Clustering GenomicTools Utility Boost::program_options)
set_target_properties(${EXE_CLASSSEQDATACREATOR} 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")
Event Timeline
Log In to Comment