生物软件安装与运行

conda安装

1.conda安装包获取
wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
2.conda文件执行安装
bash Anaconda3-2021.05-Linux-x86_64.sh
3.修改环境变量使其生效
echo 'export PATH=~/anaconda3/bin:$PATH'>>~/ .bashrc
source ~/.bashrc

aspera安装

1.aspera安装包安装
wget https://d3gcli72yxqn2z.cloudfront.net/downloads/connect/latest/bin/ibm-aspera-connect_4.2.0.42_linux.tar.gz
2.aspera解压
tar xvf ibm-aspera-connect_4.2.0.42_linux.tar.gz
3.运行安装
bash ibm-aspera-connect_4.2.0.42_linux.sh
4.添加环境变量使其生效
echo 'export PATH=~/.aspera/connect/bin/:$PATH'>>~/ .bashrc
source ~/.bashrc

763e8ebea9eaf886bb72a55ef7aa3203.png

sra-toolkit安装

1.sra-toolkit安装包安装
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.0.0/sratoolkit.3.0.0-ubuntu64.tar.gz
2.sra-toolkit解压
tar zxvf sratoolkit.3.0.0-ubuntu64.tar.gz

QQ截图20221005074355.png

3.添加环境变量并使其生效
echo 'export PATH=~/sratoolkit.3.0.0-ubuntu64/bin:$PATH' >>~/.bashrc
source ~/.bashrc
4.测试安装是否成功
prefetch -h

QQ截图20221005082237.png

5.执行vdb-config --interactive
vdb-config --interactive

QQ截图20221005083212.png

6.打开帮助面板并查看版本
prefetch -h

QQ截图20221005083334.png

fastqc安装

FastQC是在Java环境下运行的，所以在安装fastqc之前，Linux下要有相应的Java运行环境
Ubuntu系统可以通过执行以下命令安装java
sudo apt install default-jre

1.fastqc安装包安装
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip

QQ截图20221004233611.png

2. fastqc解压
   unzip fastqc_v0.11.9.zip
   
   QQ截图20221004233700.png

3.给fastqc权限
chmod 777 ~/FastQC/fastqc
4.在指定路径运行
~/FastQC/fastqc -h

QQ截图20221005000119.png

5.加入环境变量,在根目录运行
echo 'export PATH=~/FastQC:$PATH'>>~/.bashrc
source ~/.bashrc
fastqc -h

QQ截图20221005000946.png