adamjorr / kbbq Goto Github PK
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License: MIT License
reference-free base quality score recalibration
License: MIT License
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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