diff options
Diffstat (limited to 'seqwish-shared-library.diff')
| -rw-r--r-- | seqwish-shared-library.diff | 195 |
1 files changed, 0 insertions, 195 deletions
diff --git a/seqwish-shared-library.diff b/seqwish-shared-library.diff deleted file mode 100644 index be982de..0000000 --- a/seqwish-shared-library.diff +++ /dev/null @@ -1,195 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 09eafb5..a39f90f 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -7,6 +7,8 @@ project(seqwish) - # We build using c++14 - set(CMAKE_CXX_STANDARD 14) - -+include(GNUInstallDirs) -+ - set(THREADS_PREFER_PTHREAD_FLAG ON) - find_package(Threads REQUIRED) - -@@ -26,6 +28,8 @@ if(NOT DEFINED EXTRA_FLAGS) - "Extra compilation flags for C and CXX." FORCE) - endif() - -+set(SEQWISH_LINK_SHARED_LIBRARY OFF CACHE BOOL "Do not link against the libseqwish shared library") -+ - if (${CMAKE_BUILD_TYPE} MATCHES Release) - set(EXTRA_FLAGS "-Ofast ${EXTRA_FLAGS}") - set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast -@@ -82,7 +86,7 @@ include(${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>" -+ CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_CXX_FLAGS=-fPIC;-DCMAKE_C_FLAGS=-fPIC;-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" - UPDATE_COMMAND "" - INSTALL_COMMAND "") - ExternalProject_Get_property(sdsl-lite INSTALL_DIR) -@@ -203,27 +207,125 @@ set(mio_INCLUDE "${SOURCE_DIR}/include") - #set(CMAKE_BUILD_TYPE Debug) - set(CMAKE_BUILD_TYPE Release) - -+# set up our target libraries and specify its dependencies and includes -+add_library( libseqwish_static -+ ${CMAKE_SOURCE_DIR}/src/utils.cpp -+ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp -+ ${CMAKE_SOURCE_DIR}/src/main.cpp -+ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp -+ ${CMAKE_SOURCE_DIR}/src/paf.cpp -+ ${CMAKE_SOURCE_DIR}/src/sxs.cpp -+ ${CMAKE_SOURCE_DIR}/src/cigar.cpp -+ ${CMAKE_SOURCE_DIR}/src/alignments.cpp -+ ${CMAKE_SOURCE_DIR}/src/pos.cpp -+ ${CMAKE_SOURCE_DIR}/src/match.cpp -+ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp -+ ${CMAKE_SOURCE_DIR}/src/links.cpp -+ ${CMAKE_SOURCE_DIR}/src/compact.cpp -+ ${CMAKE_SOURCE_DIR}/src/dna.cpp -+ ${CMAKE_SOURCE_DIR}/src/gfa.cpp -+ ${CMAKE_SOURCE_DIR}/src/vgp.cpp -+ ${CMAKE_SOURCE_DIR}/src/exists.cpp -+ ${CMAKE_SOURCE_DIR}/src/time.cpp -+ ${CMAKE_SOURCE_DIR}/src/mmap.cpp -+ ) -+add_dependencies(libseqwish_static tayweeargs) -+add_dependencies(libseqwish_static sdsl-lite) -+add_dependencies(libseqwish_static gzipreader) -+add_dependencies(libseqwish_static mmmulti) -+add_dependencies(libseqwish_static iitii) -+add_dependencies(libseqwish_static ips4o) -+add_dependencies(libseqwish_static bbhash) -+add_dependencies(libseqwish_static atomicbitvector) -+add_dependencies(libseqwish_static atomicqueue) -+add_dependencies(libseqwish_static ska) -+add_dependencies(libseqwish_static paryfor) -+add_dependencies(libseqwish_static mio) -+target_include_directories(libseqwish_static PUBLIC -+ "${sdsl-lite_INCLUDE}" -+ "${sdsl-lite-divsufsort_INCLUDE}" -+ "${tayweeargs_INCLUDE}" -+ "${gzipreader_INCLUDE}" -+ "${ips4o_INCLUDE}" -+ "${mmmulti_INCLUDE}" -+ "${iitii_INCLUDE}" -+ "${bbhash_INCLUDE}" -+ "${atomicbitvector_INCLUDE}" -+ "${atomicqueue_INCLUDE}" -+ "${ska_INCLUDE}" -+ "${paryfor_INCLUDE}" -+ "${mio_INCLUDE}") -+target_link_libraries(libseqwish_static -+ "${sdsl-lite_LIB}/libsdsl.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" -+ "-latomic" -+ Threads::Threads -+ jemalloc -+ z) -+set_target_properties(libseqwish_static PROPERTIES OUTPUT_NAME "seqwish") -+ -+add_library( libseqwish SHARED -+ ${CMAKE_SOURCE_DIR}/src/utils.cpp -+ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp -+ ${CMAKE_SOURCE_DIR}/src/main.cpp -+ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp -+ ${CMAKE_SOURCE_DIR}/src/paf.cpp -+ ${CMAKE_SOURCE_DIR}/src/sxs.cpp -+ ${CMAKE_SOURCE_DIR}/src/cigar.cpp -+ ${CMAKE_SOURCE_DIR}/src/alignments.cpp -+ ${CMAKE_SOURCE_DIR}/src/pos.cpp -+ ${CMAKE_SOURCE_DIR}/src/match.cpp -+ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp -+ ${CMAKE_SOURCE_DIR}/src/links.cpp -+ ${CMAKE_SOURCE_DIR}/src/compact.cpp -+ ${CMAKE_SOURCE_DIR}/src/dna.cpp -+ ${CMAKE_SOURCE_DIR}/src/gfa.cpp -+ ${CMAKE_SOURCE_DIR}/src/vgp.cpp -+ ${CMAKE_SOURCE_DIR}/src/exists.cpp -+ ${CMAKE_SOURCE_DIR}/src/time.cpp -+ ${CMAKE_SOURCE_DIR}/src/mmap.cpp -+ ${CMAKE_SOURCE_DIR}/src/version.cpp -+ ) -+add_dependencies(libseqwish tayweeargs) -+add_dependencies(libseqwish sdsl-lite) -+add_dependencies(libseqwish gzipreader) -+add_dependencies(libseqwish mmmulti) -+add_dependencies(libseqwish iitii) -+add_dependencies(libseqwish ips4o) -+add_dependencies(libseqwish bbhash) -+add_dependencies(libseqwish atomicbitvector) -+add_dependencies(libseqwish atomicqueue) -+add_dependencies(libseqwish ska) -+add_dependencies(libseqwish paryfor) -+add_dependencies(libseqwish mio) -+target_include_directories(libseqwish PUBLIC -+ "${sdsl-lite_INCLUDE}" -+ "${sdsl-lite-divsufsort_INCLUDE}" -+ "${tayweeargs_INCLUDE}" -+ "${gzipreader_INCLUDE}" -+ "${ips4o_INCLUDE}" -+ "${mmmulti_INCLUDE}" -+ "${iitii_INCLUDE}" -+ "${bbhash_INCLUDE}" -+ "${atomicbitvector_INCLUDE}" -+ "${atomicqueue_INCLUDE}" -+ "${ska_INCLUDE}" -+ "${paryfor_INCLUDE}" -+ "${mio_INCLUDE}") -+target_link_libraries(libseqwish -+ "${sdsl-lite_LIB}/libsdsl.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" -+ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" -+ "-latomic" -+ Threads::Threads -+ jemalloc -+ z) -+set_target_properties(libseqwish PROPERTIES OUTPUT_NAME "seqwish") -+ - # set up our target executable and specify its dependencies and includes - add_executable(seqwish -- ${CMAKE_SOURCE_DIR}/src/utils.cpp -- ${CMAKE_SOURCE_DIR}/src/tempfile.cpp - ${CMAKE_SOURCE_DIR}/src/main.cpp -- ${CMAKE_SOURCE_DIR}/src/seqindex.cpp -- ${CMAKE_SOURCE_DIR}/src/paf.cpp -- ${CMAKE_SOURCE_DIR}/src/sxs.cpp -- ${CMAKE_SOURCE_DIR}/src/cigar.cpp -- ${CMAKE_SOURCE_DIR}/src/alignments.cpp -- ${CMAKE_SOURCE_DIR}/src/pos.cpp -- ${CMAKE_SOURCE_DIR}/src/match.cpp -- ${CMAKE_SOURCE_DIR}/src/transclosure.cpp -- ${CMAKE_SOURCE_DIR}/src/links.cpp -- ${CMAKE_SOURCE_DIR}/src/compact.cpp -- ${CMAKE_SOURCE_DIR}/src/dna.cpp -- ${CMAKE_SOURCE_DIR}/src/gfa.cpp -- ${CMAKE_SOURCE_DIR}/src/vgp.cpp -- ${CMAKE_SOURCE_DIR}/src/exists.cpp -- ${CMAKE_SOURCE_DIR}/src/time.cpp -- ${CMAKE_SOURCE_DIR}/src/mmap.cpp - ${CMAKE_SOURCE_DIR}/src/version.cpp - ) - add_dependencies(seqwish tayweeargs) -@@ -252,6 +354,11 @@ target_include_directories(seqwish PUBLIC - "${ska_INCLUDE}" - "${paryfor_INCLUDE}" - "${mio_INCLUDE}") -+if( SEQWISH_LINK_SHARED_LIBRARY ) -+ target_link_libraries( seqwish libseqwish ) -+else() -+ target_link_libraries( seqwish libseqwish_static ) -+endif() - target_link_libraries(seqwish - "${sdsl-lite_LIB}/libsdsl.a" - "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" -@@ -269,4 +376,6 @@ endif() - file(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/include) - execute_process(COMMAND bash ${CMAKE_SOURCE_DIR}/scripts/generate_git_version.sh ${CMAKE_SOURCE_DIR}/include) - --install(TARGETS seqwish DESTINATION bin) -+install(TARGETS seqwish DESTINATION "${CMAKE_INSTALL_BIDIR}") -+install(TARGETS libseqwish LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") -+install(TARGETS libseqwish_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}") |