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# Copyright (C) 2019 Intel Corporation. All rights reserved.
# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
cmake_minimum_required (VERSION 3.14)
project(bwa_wasm)
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../cmake)
################ dependencies ################
find_package(Python3 REQUIRED)
find_package(WASISDK 16.0 REQUIRED)
execute_process(
COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_LIST_DIR}/../../../test-tools/pick-up-emscripten-headers/collect_files.py --install ../include --loglevel=ERROR
WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
)
#######################################
include(ExternalProject)
################ libz ################
ExternalProject_Add(libz_src
GIT_REPOSITORY https://github.com/madler/zlib.git
GIT_TAG 04f42ceca40f73e2978b50e93806c2a18c1281fc
GIT_PROGRESS ON
GIT_SHALLOW ON
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libz
UPDATE_COMMAND ""
PATCH_COMMAND ""
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
)
################ bwa ################
ExternalProject_Add(bwa
GIT_REPOSITORY https://github.com/lh3/bwa.git
GIT_TAG 139f68fc4c3747813783a488aef2adc86626b01b
GIT_PROGRESS ON
GIT_SHALLOW ON
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/bwa
DEPENDS libz_src
UPDATE_COMMAND git clean -ffdx && git checkout -- *
&& ${CMAKE_COMMAND} -E echo "Copying pre-installed CMakeLists.txt"
&& ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.bwa_wasm.txt CMakeLists.txt
&& git apply ../bwa.patch
CONFIGURE_COMMAND ${CMAKE_COMMAND}
-DWASI_SDK_PREFIX=${WASISDK_HOME}
-DCMAKE_TOOLCHAIN_FILE=${WASISDK_TOOLCHAIN}
-DCMAKE_SYSROOT=${WASISDK_SYSROOT}
-DCMAKE_C_FLAGS=-isystem\ ${CMAKE_CURRENT_SOURCE_DIR}/../include/sse\ -isystem\ ${CMAKE_CURRENT_SOURCE_DIR}/../include/libc/musl
${CMAKE_CURRENT_SOURCE_DIR}/bwa
BUILD_COMMAND make bwa_wasm_opt -j 4
INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_if_different ./bwa.opt.wasm ${CMAKE_CURRENT_BINARY_DIR}/bwa.wasm
)
################ bwa data ################
ExternalProject_Add(bwa-kit
PREFIX bwa-kit
URL https://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.15_x64-linux.tar.bz2/download
URL_HASH SHA256=0a7b11971bc7916b68e9df35a364afe77cb3000df02ffb3a6fbd1aff9be5878c
DOWNLOAD_NAME bwakit-0.7.15_x64-linux.tar.bz2
DOWNLOAD_EXTRACT_TIMESTAMP ON
DOWNLOAD_NO_EXTRACT OFF
DOWNLOAD_NO_PROGRESS ON
UPDATE_COMMAND ""
PATCH_COMMAND ""
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_BINARY_DIR}/bwa-kit/src/bwa-kit/resource-GRCh38/hs38DH-extra.fa
${CMAKE_CURRENT_BINARY_DIR}/hs38DH-extra.fa
)
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