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 @@ -1,100 +0,0 @@ -# -# FindTileDB.cmake -# -# The MIT License -# -# Copyright (c) 2020-2021 Omics Data Automation, 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() - -#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 -lSystem") - endif() - set(HTSLIB_Debug_LDFLAGS "-g3 -gdwarf-3 ${HTSLIB_LDFLAGS}") - set(HTSLIB_Coverage_LDFLAGS "${HTSLIB_Debug_LDFLAGS}") - set(HTSLIB_Release_LDFLAGS "${HTSLIB_LDFLAGS}") - include(ExternalProject) - #Cross compiling for MacOSX - if((NOT (CMAKE_SYSTEM_NAME STREQUAL CMAKE_HOST_SYSTEM_NAME)) AND APPLE) - set(HTSLIB_OSXCROSS_COMPILE_FLAGS LIBS=${OSXCROSS_LIBS} CPPFLAGS=${OSXCROSS_CPPFLAGS} --host=${CMAKE_SYSTEM_PROCESSOR}-${CMAKE_SYSTEM}) - endif() - set(HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS "${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS} -I${OPENSSL_INCLUDE_DIR} -I${CURL_INCLUDE_DIRS}") - if(APPLE AND BUILD_DISTRIBUTABLE_LIBRARY) - set(HTSLIB_ENV "MACOSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}") - endif() - ExternalProject_Add( - htslib - DOWNLOAD_COMMAND "" - SOURCE_DIR "${HTSLIB_SOURCE_DIR}" - UPDATE_COMMAND autoreconf -i ${HTSLIB_SOURCE_DIR} - PATCH_COMMAND "" - CONFIGURE_COMMAND ${HTSLIB_ENV} ${HTSLIB_SOURCE_DIR}/configure - CFLAGS=${HTSLIB_${CMAKE_BUILD_TYPE}_CFLAGS} - LDFLAGS=${HTSLIB_${CMAKE_BUILD_TYPE}_LDFLAGS} - CC=${CMAKE_C_COMPILER} AR=${CMAKE_AR} RANLIB=${CMAKE_RANLIB} - ${HTSLIB_OSXCROSS_COMPILE_FLAGS} - --disable-lzma --disable-bz2 --disable-s3 --disable-gcs - BUILD_COMMAND ${CMAKE_COMMAND} -E make_directory cram - COMMAND ${CMAKE_COMMAND} -E make_directory test - COMMAND ${CMAKE_COMMAND} -E make_directory test/fuzz - 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} - #BUILD_IN_SOURCE 1 - INSTALL_COMMAND "" - ) - find_path(HTSLIB_INCLUDE_DIR NAMES htslib/vcf.h HINTS "${HTSLIB_SOURCE_DIR}" CMAKE_FIND_ROOT_PATH_BOTH NO_DEFAULT_PATH) - ExternalProject_Get_Property(htslib BINARY_DIR) - set(HTSLIB_DIR_IN_BUILD_DIR "${BINARY_DIR}") - set(HTSLIB_LIBRARY "${BINARY_DIR}/libhts.a") - 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 ${DEFAULT_MSG}" HTSLIB_INCLUDE_DIR HTSLIB_LIBRARY) -endif() --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -41,6 +41,11 @@ #set(FMT_ROOT_DIR "${SPDLOG_INCLUDE_DIR}" CACHE PATH "Path to fmt library") set(USING_FMT_BUNDLED_WITH_SPDLOG False CACHE BOOL "Disable if using fmt library that's not bundled with spdlog") +# add the genomicsdb-htslib bundled as a component +add_subdirectory(genomicsdb-htslib) +set(HTSLIB genomicsdb-hts) +include_directories(${CMAKE_SOURCE_DIR}/genomicsdb-htslib) + #GIT_COMMIT_HASH derived from git tag to be used as part of GENOMICSDB_VERSION execute_process( COMMAND git log -1 --format=%h @@ -60,8 +65,6 @@ option(DISABLE_MPI "Disable use of any MPI compiler/libraries") option(DISABLE_OPENMP "Disable OpenMP") -set(HTSLIB_INSTALL_DIR "" CACHE PATH "Path to htslib install directory") - #Sync the GENOMICSDB_PROTOBUF_VERSION with protobuf.version in pom.xml! set(GENOMICSDB_PROTOBUF_VERSION "3.19.4" CACHE STRING "Version of Google Protocol Buffer library") set(PROTOBUF_ROOT_DIR "$ENV{HOME}/protobuf-install/${GENOMICSDB_PROTOBUF_VERSION}" CACHE PATH "Path to installed protobuf") @@ -210,10 +213,6 @@ find_package(Spdlog REQUIRED) include_directories(${SPDLOG_INCLUDE_DIR}) -#htslib -find_package(htslib REQUIRED) -include_directories(BEFORE ${HTSLIB_INCLUDE_DIR}) - #TileDB find_package(TileDB REQUIRED) include_directories(${TILEDB_INCLUDE_DIR}) @@ -332,10 +331,6 @@ 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 ${HTSLIB_DIR_IN_BUILD_DIR}) - add_dependencies(clean-all clean-htslib) -endif() #Uninstall GenomicsDB add_custom_target( @@ -401,10 +396,7 @@ else() target_link_libraries(${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 @@ -115,6 +115,7 @@ 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()