Description: genomicsdb requires a fork of tiledb 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/CMakeLists.txt +++ b/CMakeLists.txt @@ -44,6 +44,11 @@ set(HTSLIB genomicsdb-hts) include_directories(${CMAKE_SOURCE_DIR}/genomicsdb-htslib) +# add the genomicsdb-tiledb bundled as a component +add_subdirectory(genomicsdb-tiledb) +set(TILEDB_LIBRARY tiledb_shared) +include_directories(${CMAKE_SOURCE_DIR}/genomicsdb-tiledb ${CMAKE_SOURCE_DIR}/genomicsdb-tiledb/core/include/c_api) + #GIT_COMMIT_HASH derived from git tag to be used as part of GENOMICSDB_VERSION execute_process( COMMAND git log -1 --format=%h @@ -339,10 +344,6 @@ include(UseJava) endif() -#TileDB -find_package(TileDB REQUIRED) -include_directories(${TILEDB_INCLUDE_DIR}) - #libcsv if(NOT BUILD_DISTRIBUTABLE_LIBRARY AND NOT BUILD_BINDINGS) if(USE_LIBCSV) @@ -407,13 +408,6 @@ set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3 -fvisibility=hidden") set(CMAKE_CXX_FLAGS_COVERAGE "-DDEBUG -g3 -gdwarf-3 --coverage") -#Clean all -add_custom_target(clean-all ${CMAKE_MAKE_PROGRAM} clean) -if(TILEDB_SOURCE_DIR) - add_custom_target(clean-TileDB ${CMAKE_COMMAND} -E remove_directory ${TILEDB_DIR_IN_BUILD_DIR}) - add_dependencies(clean-all clean-TileDB) -endif() - #Uninstall GenomicsDB add_custom_target( uninstall-genomicsdb --- a/cmake/Modules/FindTileDB.cmake +++ /dev/null @@ -1,84 +0,0 @@ -# -# FindTileDB.cmake -# -# The MIT License -# -# Copyright (c) 2016 MIT and Intel Corporation -# Copyright (c) 2019-2020 Omics Data Automation, Inc. -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to deal -# in the Software without restriction, including without limitation the rights -# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -# copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THE SOFTWARE. -# -# Determine compiler flags for TileDB -# Once done this will define -# TILEDB_FOUND - TileDB found - -# Update git submodule if necessary -if((DEFINED TILEDB_SOURCE_DIR) AND (NOT "${TILEDB_SOURCE_DIR}" STREQUAL "") AND (NOT EXISTS "${TILEDB_SOURCE_DIR}/CMakeLists.txt")) - MESSAGE(STATUS "Installing submodule TileDB at ${CMAKE_SOURCE_DIR}/dependencies") - execute_process( - COMMAND git submodule update --recursive --init ${CMAKE_SOURCE_DIR}/dependencies/TileDB - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} - RESULT_VARIABLE submodule_update_exit_code) - if(NOT(submodule_update_exit_code EQUAL 0)) - message(FATAL_ERROR "Failure to update git submodule TileDB") - endif() - set(TILEDB_SOURCE_DIR "${CMAKE_SOURCE_DIR}/dependencies/TileDB" CACHE PATH "Path to TileDB source directory" FORCE) -endif() - -if(CMAKE_BUILD_TYPE STREQUAL "Release") - #TileDB c-api returns a tiledb_errmsg which is what GenomicsDB should rely on - set(TILEDB_VERBOSE FALSE CACHE BOOL "Suppress TileDB Verbosity for GenomicsDB" FORCE) -endif() -set(TILEDB_DISABLE_TESTING True) - -#Zlib -find_package(ZLIB REQUIRED) - -#ZStd -set(ENABLE_ZSTD TRUE CACHE BOOL "Enable ZStd" FORCE) - -if(BUILD_DISTRIBUTABLE_LIBRARY) - set(OPENSSL_USE_STATIC_LIBS True) -endif() -find_package(OpenSSL REQUIRED) #now performed inside TileDB - -#libuuid -find_package(libuuid REQUIRED) - -include(FindPackageHandleStandardArgs) - -set(TILEDB_DISABLE_TESTS True CACHE BOOL "Disable TileDB Testing") - -#Build if TileDB source directory specified -if(TILEDB_SOURCE_DIR) - #OpenMP - if(DISABLE_OPENMP) - set(USE_OPENMP False CACHE BOOL "Disable OpenMP" FORCE) - else() - set(USE_OPENMP True CACHE BOOL "Enable OpenMP" FORCE) - endif() - - find_path(TILEDB_INCLUDE_DIR NAMES tiledb.h HINTS "${TILEDB_SOURCE_DIR}/core/include/c_api") - find_package_handle_standard_args(TileDB "Could not find TileDB headers ${DEFAULT_MSG}" TILEDB_INCLUDE_DIR) - add_subdirectory(${TILEDB_SOURCE_DIR} dependencies/TileDB EXCLUDE_FROM_ALL) -else() - find_path(TILEDB_INCLUDE_DIR NAMES "tiledb.h" HINTS "${TILEDB_INSTALL_DIR}/include") - find_library(TILEDB_LIBRARY NAMES libtiledb.a tiledb HINTS "${TILEDB_INSTALL_DIR}" "${TILEDB_INSTALL_DIR}/lib64" "${TILEDB_INSTALL_DIR}/lib") - find_package_handle_standard_args(TileDB "Could not find TileDB headers and/or libraries ${DEFAULT_MSG}" TILEDB_INCLUDE_DIR TILEDB_LIBRARY) -endif() --- a/genomicsdb-tiledb/examples/CMakeLists.txt +++ b/genomicsdb-tiledb/examples/CMakeLists.txt @@ -37,7 +37,7 @@ file(GLOB TILEDB_EXAMPLE_SOURCES "src/*.cc") # Include TileDB C API headers -include_directories("${CMAKE_SOURCE_DIR}/core/include/c_api/") +include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../core/include/c_api/") # Initialize name for example binaries set(EXAMPLE_BINS) @@ -59,7 +59,7 @@ # Run a subset of examples for Continuous Integration Testing if(NOT TILEDB_DISABLE_TESTING) - set(CI_TESTS ${CMAKE_SOURCE_DIR}/examples/run_examples.sh && + set(CI_TESTS ${CMAKE_CURRENT_SOURCE_DIR}/run_examples.sh && echo "Running diff with expected_results" && diff log ${CMAKE_SOURCE_DIR}/examples/expected_results && ${CMAKE_SOURCE_DIR}/examples/run_examples_parallel.sh) --- a/genomicsdb-tiledb/CMakeLists.txt +++ b/genomicsdb-tiledb/CMakeLists.txt @@ -40,7 +40,7 @@ endif() set(ENABLE_BLOSC False CACHE BOOL "Enable blosc compression") -set(ENABLE_ZSTD False CACHE BOOL "Enable zstd compression") +set(ENABLE_ZSTD True CACHE BOOL "Enable zstd compression") set(LIBUUID_DIR "" CACHE PATH "Path to libuuid install directory") set(HDFS_SOURCE_DIR "deps/HDFSWrapper/hadoop-hdfs-native" CACHE PATH "Path to modified libhdfs source dir") set(AZURE_FSCLIENT_SOURCE_DIR "deps/azure-storage-cpplite" CACHE PATH "Path to modified azure cpp client") --- a/src/main/CMakeLists.txt +++ b/src/main/CMakeLists.txt @@ -119,7 +119,7 @@ add_dependencies(tiledbgenomicsdb htslib) endif() target_link_libraries(tiledbgenomicsdb ${HTSLIB_LIBRARY} ${GENOMICSDB_EXTERNAL_DEPENDENCIES_LIBRARIES}) -target_link_libraries(tiledbgenomicsdb genomicsdb-hts) +target_link_libraries(tiledbgenomicsdb genomicsdb-hts tiledb_shared) if(LIBRT_LIBRARY) target_link_libraries(tiledbgenomicsdb ${LIBRT_LIBRARY}) endif()