1 files changed, 73 insertions, 0 deletions
diff --git a/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.txt b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.txt
new file mode 100644
index 000000000..5db52a38b
--- /dev/null
+++ b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.txt
@@ -0,0 +1,73 @@
+# 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
+)