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kbbq's Issues

CMake error and '--help' unrecognized

Hi, I would like to do some base recalibration for my non-model WGS bam and trying to install kbbq due to my colleague's recommendation. However, I got error right from here from installing.

cmake -DCMAKE_BUILD_TYPE=Release ..
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:30 (install):
  install TARGETS given no RUNTIME DESTINATION for executable target
  "kbbq-bin".


-- Configuring incomplete, errors occurred!
See also "/home/btx638/software/kbbq/build/CMakeFiles/CMakeOutput.log".

I saw that I need to only change the CMakeList.txt like this:

cmake_minimum_required(VERSION 3.10)

# set the project name
project(kbbq)

# specify the C++ standard
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)

# library stuff
add_subdirectory(src/minionrng)
#add_library(hts SHARED IMPORTED)
add_subdirectory(src/kbbq)

# add the executable
add_executable(kbbq-bin src/kbbq/kbbq.cc)

# force native build to enable vectorization
add_compile_options(-march=native)

# add libraries for linking
target_link_libraries(kbbq-bin kbbq)

target_include_directories(kbbq-bin PUBLIC
                          "${PROJECT_SOURCE_DIR}/include/kbbq"
                          )

set_target_properties(kbbq-bin PROPERTIES OUTPUT_NAME kbbq)

install(TARGETS kbbq-bin
	RUNTIME DESTINATION src/kbbq) ####<---- this part is my edit

and I think it works:

~/software/kbbq/build$ cmake -DCMAKE_BUILD_TYPE=Release ..
-- Configuring done
-- Generating done
-- Build files have been written to: /home/btx638/software/kbbq/build
~/software/kbbq/build$ cmake --build .
[ 20%] Built target minionrng
[ 80%] Built target kbbq
[ 90%] Linking CXX executable kbbq
[100%] Built target kbbq-bin
~/software/kbbq/build$ cmake --install .
-- Configuring done
-- Generating done
-- Build files have been written to: /home/btx638/software/kbbq/build

But when I moved the kbbq executable to path and try to run kbbq, a very long empty output appears so that I have to kill it before trying kbbq --help according the tutorial:

~$ kbbq
^C
~$ kbbq --help
kbbq: unrecognized option '--help'
[2021-05-20 19:22:26 BST]  Unknown argument ?

I think kbbq is installed based on the message but it is difficult to know if it will work. Could you please tell me if this means I have installed this correctly?

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