1. Software Introduction ​

SeqKit is an efficient, comprehensive cross-platform tool for fasta/q processing. SeqKit provides an executable binary file covering all mainstream OSs, including Windows, Linux, and MacOS X, and can be directly used without any configuration or pre-configuration.

For more information about SeqKit, visit the official website at https://bioinf.shenwei.me/seqkit/.

Language: Go

One-sentence description: fasta/q processing tool

Open source license: MIT license

Recommended version: SeqKit v2.2.0

2. Environment Requirements ​

2.1. Hardware Requirements ​

2.2. Software Requirements ​

2.3. Operating Systems ​

3. Porting Planning ​

This chapter lists the software installation paths involved in the SeqKit software porting.

Porting planning:

4. Compilation Environment Configuration ​

Prerequisites: The installation packages have been uploaded to the corresponding directories on the server using the SFTP tool.

Configuration procedure:

4.1 Kunpeng Base Software Setup ​

4.1.1 Installing from a Yum Source ​

Step 1 Add the configuration file bisheng-compiler.repo to the /etc/yum.repos.d/ directory.

cat > /etc/yum.repos.d/bisheng-compiler.repo << EOF

[bisheng-compiler]

name=bisheng-compiler

baseurl=https://repo.oepkgs.net/bisheng/aarch64/

enabled=1

gpgcheck=0

priority=100

EOF

Step 2 Download and install the RPM package of the BiSheng compiler from the Yum repository.

yum update
yum install bisheng-compiler -y

Step 3 (Optional) Clear the hash table in the current window.

If an LLVM compiler of another version is available in the system, run the following command immediately after installing the BiSheng compiler:

hash -r

This prevents the Clang command from being captured by the hash table. Otherwise, the BiSheng compiler or the open source LLVM compiler cannot be used.

Step 4 Check whether the installation is successful.

After the installation is complete, run the following command to verify the BiSheng compiler's version:

clang -v

If the command output contains the BiSheng compiler version information, the installation is successful.

4.1.2 Software Package Installation Mode ​

Step 1 Make preparations.

Download the BiSheng compiler on the BiSheng compiler page and upload it to the server.

Software package download: https://www.hikunpeng.com/en/developer/devkit/compiler/bisheng

Step 2 Install the environment dependency items of the BiSheng compiler.

yum install -y gcc glibc libatomic bc tar

Step 3 Create the installation directory of the BiSheng compiler.

mkdir -p /usr/local/bisheng

Note: In the preceding command, /usr/local/ is an example. Replace it with an actual path.

Step 4 Download the BiSheng compiler package and decompress it.

cd /usr/local/bisheng
wget https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz --no-check-certificate
tar -zxvf bisheng-compiler-2.1.0-aarch64-linux.tar.gz

After the decompression, the bisheng-compiler-2.1.0-aarch64-linux directory is generated in the current directory.

Step 5 Install the environment-modules tool.

yum install environment-modules -y
source /etc/profile

Step 6 Create an environment variable configuration file.

vi /usr/local/bisheng/bisheng_modulefiles

The following content is added:

#%Module1.0
conflict bisheng
prepend-path PATH /usr/local/bisheng/bisheng-compiler-2.1.0-aarch64-linux/bin
prepend-path LD_LIBRARY_PATH /usr/local/bisheng/bisheng-compiler-2.1.0-aarch64-linux/lib

Step 7 Load environment variables in the current shell.

module use /usr/local/bisheng/
module load /usr/local/bisheng/bisheng_modulefiles

Note: (Optional) To prevent variables from being imported every time a shell is opened, you are advised to write the environment variables to the system configuration file.

vi /etc/profile

The following content is added:

module use /usr/local/bisheng/
module load /usr/local/bisheng/bisheng_modulefiles

Step 8 Make the environment variables take effect.

source /etc/profile

Step 9 (Optional) Clear the hash table in the current window.

If an LLVM compiler of another version is available in the system, run the following command immediately after installing the BiSheng compiler:

hash -r

This prevents the Clang command from being captured by the hash table. Otherwise, the BiSheng compiler or the open source LLVM compiler cannot be used.

Step 10 Check whether the installation is successful.

After the installation is complete, run the following command to verify the BiSheng compiler's version:

clang -v

If the command output contains the BiSheng compiler version information, the installation is successful.

----End

4.2 Dependency Installation ​

Step 1 Install the dependency package from a Yum source.

 yum -y install git gcc gcc-c++ vim
 source /etc/profile

4.3 Go Environment Deployment ​

Step 1 Use PuTTY to log in to the server as user root. Step 2 Go to the /home directory.

cd /home

Step 3 Obtain the Go package.

wget https://dl.google.com/go/go1.18.linux-arm64.tar.gz

Step 4 Create an installation path.

mkdir -p /usr/local/seqkit/

Step 5 Decompress the Go installation package.

tar -zxvf go1.18.linux-arm64.tar.gz -C /usr/local/seqkit/

Note: Decompress the package based on the actual package name. Step 6 Configure environment variables.

vi /usr/local/seqkit/go/go_modulefiles

The following content is added:

#%Module1.0
conflict go
set GO /usr/local/seqkit/go
setenv GO $GO
prepend-path PATH $GO/bin

Step 7 Load environment variables.

module use /usr/local/seqkit/go
module load /usr/local/seqkit/go/go_modulefiles

Step 8 (Optional) To prevent variables from being imported every time a shell is opened, write the environment variables to the system configuration file.

vi /etc/profile

The following content is added:

module use /usr/local/seqkit/go
module load /usr/local/seqkit/go/go_modulefiles

Step 9 Make the environment variables take effect.

source /etc/profile

Step 10 Run the following command to check the installation path:

ls /usr/local/seqkit/go/

Step 11 Check the version number.

go version

Step 12 Replace the Go source with the source from China.

go env -w GOPROXY=https://goproxy.cn

5. Source Code Obtaining ​

Step 1 Download the SeqKit installation package v2.2.0.tar.gz.

Download address: https://github.com/shenwei356/seqkit/archive/refs/tags/v2.2.0.tar.gz

6. Compilation and Installation ​

Step 1 Use PuTTY to log in to the server as user root. Step 2 Go to the /home directory.

cd /home

Step 3 Obtain the source package.

wget https://github.com/shenwei356/seqkit/archive/refs/tags/v2.2.0.tar.gz

Step 4 Decompress the package.

mv v2.2.0.tar.gz seqkit-2.2.0.tar.gz && tar -xvf seqkit-2.2.0.tar.gz

Step 5 Configure the compilation.

go env -w CXX=clang++
go env -w CC=clang
go env

Step 6 Perform the compilation.

cd seqkit-2.2.0/seqkit/
go build

Step 7 Perform the installation.

mkdir -p /usr/local/seqkit/seqkit/bin
cp ./seqkit /usr/local/seqkit/seqkit/bin
ls /usr/local/seqkit/seqkit/bin

Step 8 Set environment variables.

vi /usr/local/seqkit/seqkit/seqkit_modulefiles

The following content is added:

#%Module1.0
conflict seqkit 
set SEQKIT /usr/local/seqkit/seqkit
setenv SEQKIT $SEQKIT
prepend-path PATH $SEQKIT/bin

Step 9 Load environment variables.

module use /usr/local/seqkit/seqkit
module load /usr/local/seqkit/seqkit/seqkit_modulefiles

Step 10 (Optional) To prevent variables from being imported every time a shell is opened, write the environment variables to the system configuration file.

vi /etc/profile

The following content is added:

module use /usr/local/seqkit/seqkit
module load /usr/local/seqkit/seqkit/seqkit_modulefiles

Step 11 Make the environment variables take effect.

source /etc/profile

----End

7. Running and Verification ​

Data source: The test verification data and scripts are obtained from the SeqKit source package. For details about how to download the source package, see section 5. The data and scripts are stored in:

Step 1 Use PuTTY to log in to the server as user root. Step 2 Go to the source package directory.

cd /home/seqkit-2.2.0/

Step 3 Copy the test verification script to the current directory.

cp tests/test.sh ./

Step 4 Edit the script, delete the SeqKit generation command, and change the SeqKit path in the script to the installation path.

vi test.sh

Note: The installation path varies according to the actual situation. Before the change:

After the change:

Step 5 Run the following command to check the running of SeqKit:

bash test.sh

Step 6 View SeqKit details. seqkit --help

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8. Change History ​