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}")
