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|
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 <pgt@debian.org>
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()
|
