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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 3.13.4)
project(BlooMine)
## set compiler and flags
set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread")
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/../bin)
## find and include boost program_options library
find_package( Boost 1.40 COMPONENTS program_options REQUIRED )
include_directories( ${Boost_INCLUDE_DIR} )
## executables and source files
add_executable(BlooMine ./src/BlooMine.cpp)
target_link_libraries( BlooMine LINK_PUBLIC ${Boost_LIBRARIES} )
## install rules
install(TARGETS BlooMine DESTINATION bin)
## test module
enable_testing()
## run test
add_test(NAME Runs COMMAND BlooMine)
set_tests_properties(Runs
PROPERTIES PASS_REGULAR_EXPRESSION "Too few argument provided!*")
## help test
add_test(NAME Help COMMAND BlooMine --help)
set_tests_properties(Help
PROPERTIES PASS_REGULAR_EXPRESSION "Allowed options:*")
## test data run
add_test(NAME test_run COMMAND BlooMine --target_fasta ../test/targets/D614G.fa --fastq ../test/fqs/testFQ.fq --threads 2)
set_tests_properties(test_run
PROPERTIES PASS_REGULAR_EXPRESSION "*Finished screening.*")