Merge branch 'master' of /home/git/public/guix-bioinformatics

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}")