一、软件介绍

cas-offinder是一款生命科学应用，用于搜索 CRISPR/Cas 衍生的 RNA 引导内切酶 (RGEN) 的潜在脱靶位点。

一、获取源码

cd /path/to

wget https://github.com/snugel/cas-offinder/archive/refs/tags/3.0.0b3.tar.gz -O cas-offinder-3.0.0b3.tar.gz

二、下载系统依赖

处理器：鲲鹏920系列

操作系统：openEuler 22.03 SP2

yum源：openEuler官方网络源

编译器：llvm编译器

安装所需系统依赖：cmake doxygen libxml2-devel xz libedit-devel swig hwloc-devel python3 python3-devel python3-pip lua-* clang doxygen glew glew-devel freetype freetype-devel libX11-devel libXrandr-devel ocl-icd-devel ocl-icd opencl-headers

三、编译步骤

1.1 安装依赖llvm

cd /path/to/

wget https://github.com/llvm/llvm-project/archive/llvmorg-17.0.1.tar.gz

tar -xf llvmorg-17.0.1.tar.gz

cd llvm-project-llvmorg-17.0.1

cd llvm

mkdir build

cd build

export CC=clang CXX=clang++

cmake ../ -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=/path/to/llvm -DCMAKE_BUILD_TYPE=Debug -DLLVM_ENABLE_RTTI=ON -DLLVM_TARGETS_TO_BUILD=all -DLLVM_ENABLE_PROJECTS="lldb;clang;clang-tools-extra;flang;lld;polly" -DLLVM_ENABLE_RUNTIMES="openmp;compiler-rt;libunwind" -DRUNTIMES_CMAKE_ARGS=-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON

make -j（此处编译比较久，若无报错，请耐心等待）

make install

export PATH=/path/to/llvm/bin:$PATH

export LD_LIBRARY_PATH=/path/to/llvm/lib:$LD_LIBRARY_PATH

1.2 安装依赖SPIRV-LLVM-Translator

cd /path/to

wget https://github.com/KhronosGroup/SPIRV-LLVM-Translator/archive/refs/tags/v17.0.0.tar.gz

tar -xf v17.0.0.tar.gz

cd SPIRV-LLVM-Translator-17.0.0

mkdir build

cd build

cmake ../ -DCMAKE_INSTALL_PREFIX=/path/to/llvm

make llvm-spirv -j

make install

1.3 安装依赖OpenCL-SDK

cd /path/to

git clone --recursive https://github.com/KhronosGroup/OpenCL-SDK.git

（注意此处带了参数--recursive，如果因github网络波动下载失败，多试几次）

cd OpenCL-SDK

mkdir build

cd build

cmake ../ -DCMAKE_INSTALL_PREFIX=/path/to/OpenCL -DBUILD_TESTING=OFF -DBUILD_DOCS=OFF -DBUILD_EXAMPLES=OFF -DBUILD_TESTS=OFF -DOPENCL_SDK_BUILD_SAMPLES=OFF -DOPENCL_SDK_TEST_SAMPLES=OFF

make -j

make install

export PATH=/path/to/OpenCL/bin:$PATH

export LD_LIBRARY_PATH=/path/to/OpenCL/lib64:$LD_LIBRARY_PATH

1.4 安装依赖pocl

cd /path/to

wget https://github.com/pocl/pocl/archive/refs/tags/v5.0.tar.gz -O pocl-v5.0.tar.gz

tar xf pocl-v5.0.tar.gz

cd pocl-5.0

mkdir build

cd build

cmake ../ -DCMAKE_INSTALL_PREFIX=/path/to/pocl -DCMAKE_BUILD_TYPE=Release -DINSTALL_OPENCL_HEADERS=OFF -DENABLE_LLVM=ON -DSTATIC_LLVM=static -DENABLE_ICD=ON

make -j

make install

export PATH=/path/to/pocl/bin:$PATH

export LD_LIBRARY_PATH=/path/to/pocl/lib64:$LD_LIBRARY_PATH

export OCL_ICD_VENDORS=/path/to/pocl/etc/OpenCL/vendors

简单验证测试      

poclcc -l

1.5 安装软件cas-offinder

cd /path/to

tar xf cas-offinder-3.0.0b3.tar.gz

cd cas-offinder-3.0.0b3

mkdir build

cd build

cmake .. -DOpenCL_LIBRARY=/path/to/OpenCL/lib64/libOpenCL.so -DOpenCL_INCLUDE_DIR=/path/to/OpenCL/include

make -j

四、验证与测试

cd /path/to

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

mkdir human_hg19

tar xf chromFa.tar.gz -C /path/to/human_hg19

选取部分算例测试

mkdir human_hg19_chrM_chrX_chrY

cp human_hg19/chrM.fa human_hg19_chrM_chrX_chrY

cp human_hg19/chrX.fa human_hg19_chrM_chrX_chrY

cp human_hg19/chrY.fa human_hg19_chrM_chrX_chrY

cd human_hg19_chrM_chrX_chrY

新建input.txt

/path/to/human_hg19_chrM_chrX_chrY

NNNNNNNNNNNNNNNNNNNNNRG 2 1

GGCCGACCTGTCGCTGACGCNNN 5

CGCCAGCGTCAGCGACAGGTNNN 5

ACGGCGCCAGCGTCAGCGACNNN 5

GTCGCTGACGCTGGCGCCGTNNN 5

（注意：该input.txt文件末尾不能留空行）

/path/to/cas-offinder-3.0.0b3/build/cas-offinder input.txt C ouput.txt