diff options
Diffstat (limited to 'biology/seqwish/files/patch-CMakeLists.txt')
| -rw-r--r-- | biology/seqwish/files/patch-CMakeLists.txt | 52 |
1 files changed, 47 insertions, 5 deletions
diff --git a/biology/seqwish/files/patch-CMakeLists.txt b/biology/seqwish/files/patch-CMakeLists.txt index 3c6ca1d2757f..1c3e0fd7147d 100644 --- a/biology/seqwish/files/patch-CMakeLists.txt +++ b/biology/seqwish/files/patch-CMakeLists.txt @@ -1,14 +1,56 @@ +# unbundle sdsl-lite + --- CMakeLists.txt.orig 2023-04-19 15:25:32 UTC +++ CMakeLists.txt -@@ -256,9 +256,9 @@ target_link_libraries(seqwish - "${sdsl-lite_LIB}/libsdsl.a" - "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" - "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" +@@ -79,18 +79,15 @@ include_directories("${PROJECT_SOURCE_DIR}") + # Add external projects + include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) + +-# sdsl-lite (full build using its cmake config) +-ExternalProject_Add(sdsl-lite +- SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite" +- CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" +- UPDATE_COMMAND "" +- INSTALL_COMMAND "") +-ExternalProject_Get_property(sdsl-lite INSTALL_DIR) +-set(sdsl-lite_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/include") +-set(sdsl-lite-divsufsort_INCLUDE "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/include") +-set(sdsl-lite_LIB "${INSTALL_DIR}/src/sdsl-lite-build/lib") +-set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdivsufsort/lib") ++# sdsl-lite - use system library ++find_package(PkgConfig REQUIRED) ++pkg_check_modules(SDSL REQUIRED sdsl-lite) ++pkg_check_modules(DIVSUFSORT REQUIRED libdivsufsort) ++pkg_check_modules(DIVSUFSORT64 REQUIRED libdivsufsort64) ++set(sdsl-lite_INCLUDE "${SDSL_INCLUDE_DIRS}") ++set(sdsl-lite-divsufsort_INCLUDE "${DIVSUFSORT_INCLUDE_DIRS}") ++link_directories(${SDSL_LIBRARY_DIRS} ${DIVSUFSORT_LIBRARY_DIRS} ${DIVSUFSORT64_LIBRARY_DIRS}) + + # taywee's C++ args library, header only + ExternalProject_Add(tayweeargs + SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args" +@@ -227,7 +224,6 @@ add_executable(seqwish + ${CMAKE_SOURCE_DIR}/src/version.cpp + ) + add_dependencies(seqwish tayweeargs) +-add_dependencies(seqwish sdsl-lite) + add_dependencies(seqwish gzipreader) + add_dependencies(seqwish mmmulti) + add_dependencies(seqwish iitii) +@@ -253,11 +249,11 @@ target_include_directories(seqwish PUBLIC + "${paryfor_INCLUDE}" + "${mio_INCLUDE}") + target_link_libraries(seqwish +- "${sdsl-lite_LIB}/libsdsl.a" +- "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" +- "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" - "-latomic" ++ ${SDSL_LIBRARIES} ++ ${DIVSUFSORT_LIBRARIES} ++ ${DIVSUFSORT64_LIBRARIES} + #"-latomic" Threads::Threads - jemalloc + #jemalloc z) if (BUILD_STATIC) - #set(CMAKE_EXE_LINKER_FLAGS "-static") |