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authorShepherd on Tux022024-06-20 08:37:15 -0500
committerShepherd on Tux022024-06-20 08:37:15 -0500
commitfe5fd5cb23907f8e37edafda96bafa608a3e0e7f (patch)
tree0b4cec2038dde07fe26f1c6882369f36a9545a19 /seqwish-shared-library.diff
parentf0f8dc84eca7088177797f84db05314537615c77 (diff)
parent0362ee068a39ce9a5fd6f0fba9cd5586211f07f1 (diff)
downloadguix-bioinformatics-fe5fd5cb23907f8e37edafda96bafa608a3e0e7f.tar.gz
Merge branch 'master' of /home/git/public/guix-bioinformatics
Diffstat (limited to 'seqwish-shared-library.diff')
-rw-r--r--seqwish-shared-library.diff195
1 files changed, 195 insertions, 0 deletions
diff --git a/seqwish-shared-library.diff b/seqwish-shared-library.diff
new file mode 100644
index 0000000..be982de
--- /dev/null
+++ b/seqwish-shared-library.diff
@@ -0,0 +1,195 @@
+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}")