diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 32 | ||||
| -rw-r--r-- | seqwish-shared-library.diff | 195 |
2 files changed, 216 insertions, 11 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 285b01d..50c207d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1609,7 +1609,8 @@ runApp(launch.browser=0, port=4208)~%\n" (file-name (git-file-name name version)) (sha256 (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x")) - (patches (search-patches "seqwish-paryfor-riscv.diff")) + (patches (search-patches "seqwish-paryfor-riscv.diff" + "seqwish-shared-library.diff")) (snippet #~(begin (use-modules (guix build utils)) @@ -1626,14 +1627,24 @@ runApp(launch.browser=0, port=4208)~%\n" (build-system cmake-build-system) (arguments `(#:configure-flags - '(,@(if (target-x86?) - ;; This is the minimum needed to compile on x86_64, and is a - ;; subset of any other optimizations which might be applied. - '("-DCMAKE_C_FLAGS=-mcx16" - "-DCMAKE_CXX_FLAGS=-mcx16") - '())) + (cons* ,@(if (target-x86?) + ;; This is the minimum needed to compile on x86_64, and is a + ;; subset of any other optimizations which might be applied. + '("-DCMAKE_C_FLAGS=-mcx16" + "-DCMAKE_CXX_FLAGS=-mcx16") + '()) + '("-DSEQWISH_LINK_SHARED_LIBRARY=ON")) #:phases (modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + ;; This stashes the build version in the executable. + (mkdir "include") + (substitute* "CMakeLists.txt" + (("^execute_process") "#execute_process")) + (with-output-to-file "include/seqwish_git_version.hpp" + (lambda () + (format #t "#define SEQWISH_GIT_VERSION \"~a\"~%" ,version))))) (add-after 'unpack 'link-with-some-shared-libraries (lambda* (#:key inputs #:allow-other-keys) (substitute* '("CMakeLists.txt" @@ -1642,11 +1653,10 @@ runApp(launch.browser=0, port=4208)~%\n" (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") (("\\$\\{sdsl-lite_INCLUDE\\}") - (string-append (assoc-ref inputs "sdsl-lite") - "/include/sdsl")) + (search-input-directory inputs "/include/sdsl")) (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") - (string-append (assoc-ref inputs "libdivsufsort") - "/include"))))) + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) ;; Add seqwish to the PATH for the tests. 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}") |