基因数据分析软件迁移-Sambamba-0.7.0

系统依赖安装

yum install libconfig libconfig-devel python3-devel cmake3 -y

1.1 如果系统pagesize修改为4k，需要源码安装libconfig，否则安装失败会破坏操作系统

1.1.1 下载软件包

wget https://github.com/hyperrealm/libconfig/archive/refs/tags/v1.7.3.tar.gz

1.1.2 解压软件包

tar –xf v1.7.3.tar.gz

1.1.3 进入解压目录

cd libconfig-1.7.3

1.1.4 编译安装

mkdir build && cd build

cmake ..

make –j 96

make install

1.2 安装llvm-3.5

1.2.1 下载软件包

wget https://github.com/llvm/llvm-project/archive/refs/tags/llvmorg-3.5.0.tar.gz

1.2.2 解压软件包

tar -xf llvmorg-3.5.0.tar.gz

1.2.3 进入解压目录

cd llvmorg-3.5.0

1.2.3 编译安装(注意替换-DCMAKE_INSTALL_PREFIX为期望的目录)

cmake -G “Unix Makefiles” -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/llvmorg-3.5.0 -DLLVM_TARGETS_TO_BUILD='AArch64’ -DCOMPILER_RT_INCLUDE_TESTS=OFF -DLLVM_INCLUDE_TESTS=OFF

make -j 96 && make install

1.3 安装ldc-0.17.6

1.3.1 下载软件包

wget https://objects.githubusercontent.com/github-production-release-asset-2e65be/2174666/cd11aa80-a741-11e8-8675-cad895bd1044?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220106%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220106T122258Z&X-Amz-Expires=300&X-Amz-Signature=b0178ff749d43294fc2256dd854371c58fb1148ee6e409adf6cf062750145195&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=2174666&response-content-disposition=attachment%3B%20filename%3Dldc-0.17.6-src.tar.gz&response-content-type=application%2Foctet-stream

1.3.2 解压软件包

tar -xf ldc-0.17.6-src.tar.gz

1.3.3 进入解压目录

cd ldc-0.17.6-src

1.3.4 编译安装

export PATH={llvm-3.5.0安装目录}/bin:${PATH}

export LD_LIBRARY_PATH={llvm-3.5.0安装目录}/lib:${LD_LIBRARY_PATH}

mkdir build && cd build

cmake3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/opt/ldc-0.17.6 ..

make –j 96 make install

1.4 参考步骤1.2安装llvm-4.0

1.5 参考步骤1.3安装ldc-1.17.0,替换cmake命令如下：

export PATH={ldc-0.17.6安装目录}/bin:${PATH}

export LD_LIBRARY_PATH={ldc-0.17.6安装目录}/lib:${LD_LIBRARY_PATH}

cmake3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX={ldc-1.17.0安装目录} -DLLVM_ROOT_DIR={llvm4.0安装目录} -DD_COMPILER={ldc-0.17.6安装目录}/bin/ldmd2

1.6 下载软件包

wget https://codeload.github.com/biod/sambamba/tar.gz/refs/tags/v0.7.0 -O sambamba-0.7.0.tar.gz

1.6.1 解压软件包

tar -xf sambamba-0.7.0.tar.gz

1.6.2 进入解压目录

cd sambamba-0.7.0

1.6.3 下载外部工程

wget https://github.com/lz4/lz4/archive/b3692db46d2b23a7c0af2d5e69988c94f126e10a.zip

wget https://codeload.github.com/lomereiter/htslib/zip/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5

wget https://codeload.github.com/biod/BioD/zip/0d06e291b03bd32b3ed0f188f99d0e801c7ee369

1.6.4 解压lz4，htslib，BioD

unzip lz4-b3692db46d2b23a7c0af2d5e69988c94f126e10a.zip

unzip htslib2f3c3ea7b301f9b45737a793c0b2dcf0240e5e.zip

unzip BioD0d06e291b03bd32b3ed0f188f99d0e801c7ee369.zip

1.6.5 清理原始空目录

rmdir lz4

rmdir htslib

rmdir BioD

1.6.6 重命名lz4，htslib，BioD

mv lz4-b3692db46d2b23a7c0af2d5e69988c94f126e10a lz4

mv htslib2f3c3ea7b301f9b45737a793c0b2dcf0240e5e.zip htslib

mv BioD0d06e291b03bd32b3ed0f188f99d0e801c7ee369.zip BioD

1.6.7 编译

make –j 96

1.6.8 验证

基因测序

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