Description: genomicsdb needs a fork of htslib, which is too different from the Debian-packaged one. We provide it as a component. Author: Pierre Gruet Forwarded: not-needed Last-Update: 2022-07-26 --- a/cmake/Modules/Findhtslib.cmake +++ /dev/null @@ -1,130 +0,0 @@ -# -# FindTileDB.cmake -# -# The MIT License -# -# Copyright (c) 2020-2021 Omics Data Automation, Inc. -# Copyright (c) 2023 dātma, inc™ -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# Determine compiler flags for htslib -# Once done this will define -# HTSLIB_FOUND - htslib found - -include(FindPackageHandleStandardArgs) - -# Update git submodule if necessary -if((DEFINED HTSLIB_SOURCE_DIR) AND (NOT "${HTSLIB_SOURCE_DIR}" STREQUAL "") AND (NOT EXISTS "${HTSLIB_SOURCE_DIR}/htslib/vcf.h")) - MESSAGE(STATUS "Installing submodule htslib at ${CMAKE_SOURCE_DIR}/dependencies") - execute_process( - COMMAND git submodule update --init ${CMAKE_SOURCE_DIR}/dependencies/htslib - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} - RESULT_VARIABLE submodule_update_exit_code) - if(NOT(submodule_update_exit_code EQUAL 0)) - message(FATAL_ERROR "Failure to update git submodule htslib") - endif() - set(HTSLIB_SOURCE_DIR "${CMAKE_SOURCE_DIR}/dependencies/htslib" CACHE PATH "Path to htslib source directory" FORCE) -endif() - -function(build_universal_htslib arch1 arch2) - add_custom_target(htslib COMMAND - echo "Building universal library in HTSLIB_INSTALL_DIR=${HTSLIB_INSTALL_DIR} for ${arch1} ${arch2}" && - lipo -create ${HTSLIB_BUILD_PREFIX}_${arch1}/libhts.a ${HTSLIB_BUILD_PREFIX}_${arch2}/libhts.a -output ${HTSLIB_LIBRARY}) - add_dependencies(htslib htslib_${arch1} htslib_${arch2}) -endfunction() - -function(build_htslib arch) - if (NOT ${arch} STREQUAL "") - set(SUFFIX _${arch}) - set(ARCH_C_FLAGS "-arch ${arch} ${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS}") - if (NOT arch STREQUAL CMAKE_SYSTEM_PROCESSOR) - set(ARCH_HOST_FLAGS "--host=${CMAKE_SYSTEM_PROCESSOR}") - endif() - else() - set(ARCH_C_FLAGS ${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS}) - endif() - ExternalProject_Add(htslib${SUFFIX} - PREFIX ${HTSLIB_BUILD_PREFIX}${SUFFIX} - DOWNLOAD_COMMAND "" - SOURCE_DIR ${HTSLIB_SOURCE_DIR} - BINARY_DIR ${HTSLIB_BUILD_PREFIX}${SUFFIX} - UPDATE_COMMAND autoreconf -i ${HTSLIB_SOURCE_DIR} - PATCH_COMMAND "" - CONFIGURE_COMMAND ${HTSLIB_ENV} ${HTSLIB_SOURCE_DIR}/configure ${ARCH_HOST_FLAGS} - CFLAGS=${ARCH_C_FLAGS} - LDFLAGS=${HTSLIB_${CMAKE_BUILD_TYPE}_LDFLAGS} - CC=${CMAKE_C_COMPILER} AR=${CMAKE_AR} RANLIB=${CMAKE_RANLIB} - --disable-lzma --disable-bz2 --disable-s3 --disable-gcs --without-libdeflate - BUILD_COMMAND - COMMAND ${CMAKE_COMMAND} -E make_directory cram - COMMAND ${CMAKE_COMMAND} -E copy ${HTSLIB_SOURCE_DIR}/version.sh . - COMMAND ${HTSLIB_ENV} $(MAKE) -f ${HTSLIB_SOURCE_DIR}/Makefile VPATH=${HTSLIB_SOURCE_DIR} SOURCE_DIR=${HTSLIB_SOURCE_DIR} AR=${CMAKE_AR} libhts.a - INSTALL_COMMAND "" - ) -endfunction() - -#Build if htslib source directory specified -if(HTSLIB_SOURCE_DIR) - set(HTSLIB_Debug_CFLAGS " -Wall -fPIC -DDEBUG -g3 -gdwarf-3 -DVCF_ALLOW_INT64=1") #will be picked if compiling in debug mode - if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") - set(HTSLIB_Debug_CFLAGS "${HTSLIB_Debug_CFLAGS} -Wno-expansion-to-defined -Wno-nullability-completeness") - endif() - set(HTSLIB_Coverage_CFLAGS "${HTSLIB_Debug_CFLAGS}") - set(HTSLIB_Release_CFLAGS " -Wall -fPIC -O3 -DVCF_ALLOW_INT64=1") - if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") - set(HTSLIB_Release_CFLAGS "${HTSLIB_Release_CFLAGS} -Wno-expansion-to-defined -Wno-nullability-completeness") - endif() - if(APPLE) - set(HTSLIB_LDFLAGS " -L /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib") - endif() - set(HTSLIB_Debug_LDFLAGS "-g3 -gdwarf-3 ${HTSLIB_LDFLAGS}") - set(HTSLIB_Coverage_LDFLAGS "${HTSLIB_Debug_LDFLAGS}") - set(HTSLIB_Release_LDFLAGS "${HTSLIB_LDFLAGS}") - - include(ExternalProject) - set(HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS "${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS} -I${OPENSSL_INCLUDE_DIR} -I${CURL_INCLUDE_DIRS}") - set(HTSLIB_LIBRARY ${CMAKE_BINARY_DIR}/libhts.a) - - if(APPLE) - if(BUILD_DISTRIBUTABLE_LIBRARY) - set(HTSLIB_ENV "MACOSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}") - endif() - endif() - set(HTSLIB_BUILD_PREFIX ${CMAKE_BINARY_DIR}/dependencies/htslib) - set(HTSLIB_LIBRARY ${CMAKE_BINARY_DIR}/libhts.a) - if(APPLE AND CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" AND CMAKE_OSX_ARCHITECTURES MATCHES "arm64") - build_htslib("x86_64") - build_htslib("arm64") - build_universal_htslib("x86_64" "arm64") - elseif(APPLE AND CMAKE_OSX_ARCHITECTURES) - build_htslib(${CMAKE_OSX_ARCHITECTURES}) - add_custom_target(htslib COMMAND cp ${HTSLIB_BUILD_PREFIX}_${CMAKE_OSX_ARCHITECTURES}/libhts.a ${HTSLIB_LIBRARY}) - add_dependencies(htslib htslib_${CMAKE_OSX_ARCHITECTURES}) - else() - build_htslib("") - add_custom_command(TARGET htslib POST_BUILD COMMAND cp ${HTSLIB_BUILD_PREFIX}/libhts.a ${HTSLIB_LIBRARY} VERBATIM) - endif() - find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_SOURCE_DIR}" CMAKE_FIND_ROOT_PATH_BOTH NO_DEFAULT_PATH) - find_package_handle_standard_args(htslib "Could not find htslib headers ${DEFAULT_MSG}" HTSLIB_INCLUDE_DIR) -else() - find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_INSTALL_DIR}") - find_library(HTSLIB_LIBRARY NAMES libhts.a hts HINTS "${HTSLIB_INSTALL_DIR}") - find_package_handle_standard_args(htslib "Could not find htslib headers and/or libraries ${DEFAULT_MSG}" HTSLIB_INCLUDE_DIR HTSLIB_LIBRARY) -endif() --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -39,6 +39,11 @@ set(GENOMICSDB_RELEASE_VERSION "1.5.4-SNAPSHOT" CACHE STRING "GenomicsDB release version") #used in Maven builds string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" GENOMICSDB_BASE_VERSION "${GENOMICSDB_RELEASE_VERSION}") +# add the genomicsdb-htslib bundled as a component +add_subdirectory(genomicsdb-htslib) +set(HTSLIB genomicsdb-hts) +include_directories(${CMAKE_SOURCE_DIR}/genomicsdb-htslib) + #GIT_COMMIT_HASH derived from git tag to be used as part of GENOMICSDB_VERSION execute_process( COMMAND git log -1 --format=%h @@ -79,8 +84,6 @@ option(DISABLE_OPENMP "Disable OpenMP") option(DISABLE_TOOLS "Disable build of tools") -set(HTSLIB_INSTALL_DIR "" CACHE PATH "Path to htslib install directory") - #Sync the GENOMICSDB_PROTOBUF_VERSION with protobuf.version in pom.xml! set(GENOMICSDB_PROTOBUF_VERSION "3.21.7" CACHE STRING "Version of Google Protocol Buffer library") set(PROTOBUF_ROOT_DIR "$ENV{HOME}/protobuf-install/${GENOMICSDB_PROTOBUF_VERSION}" CACHE PATH "Path to installed protobuf") @@ -278,10 +281,6 @@ find_package(Spdlog REQUIRED) include_directories(${SPDLOG_INCLUDE_DIR}) -#htslib -find_package(htslib REQUIRED) -include_directories(BEFORE ${HTSLIB_INCLUDE_DIR}) - #librt find_library(LIBRT_LIBRARY rt) @@ -414,10 +413,6 @@ add_custom_target(clean-TileDB ${CMAKE_COMMAND} -E remove_directory ${TILEDB_DIR_IN_BUILD_DIR}) add_dependencies(clean-all clean-TileDB) endif() -if(HTSLIB_SOURCE_DIR) - add_custom_target(clean-htslib ${CMAKE_COMMAND} -E remove_directory ${HTSLIB_DIR_IN_BUILD_DIR}) - add_dependencies(clean-all clean-htslib) -endif() #Uninstall GenomicsDB add_custom_target( @@ -483,10 +478,7 @@ else() target_link_libraries(${target} ${TILEDB_LIBRARY}) endif() - if(HTSLIB_SOURCE_DIR) - add_dependencies(${target} htslib) - endif() - target_link_libraries(${target} ${HTSLIB_LIBRARY}) + target_link_libraries(${target} ${HTSLIB}) if(LIBCSV_FOUND) target_link_libraries(${target} ${LIBCSV_LIBRARY}) endif() --- a/src/main/CMakeLists.txt +++ b/src/main/CMakeLists.txt @@ -119,6 +119,7 @@ add_dependencies(tiledbgenomicsdb htslib) endif() target_link_libraries(tiledbgenomicsdb ${HTSLIB_LIBRARY} ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES}) +target_link_libraries(tiledbgenomicsdb genomicsdb-hts) if(LIBRT_LIBRARY) target_link_libraries(tiledbgenomicsdb ${LIBRT_LIBRARY}) endif()