在目录/home/user/biosoft下运行
# 安装GitHub数据库
git clone https://github.com/biocore/sortmerna.git
# 安装SortMeRNA
# get the distro
wget https://github.com/biocore/sortmerna/releases/download/v4.2.0/sortmerna-4.2.0-Linux.sh
# view the installer usage
bash sortmerna-4.2.0-Linux.sh --help
# run the installer
bash sortmerna-4.2.0-Linux.sh --skip-license
# check the installed binaries
ls -lrt /home/MYM/biosoft/bin/
# set PATH
export PATH="$PATH:/home/user/biosoft/bin"
# test the installation
sortmerna --version
# view help
sortmerna -h
常用参数.png
# 创建脚本
touch sortmerna.sh
vim sortmerna.sh
# 按 i 进行编辑
#!/bin/sh
sortmerna -ref data/rRNA_databases/silva-bac-16s-id90.fasta -ref data/rRNA_databases/silva-bac-23s-id98.fasta -ref data/rRNA_databases/silva-arc-16s-id95.fasta -ref data/rRNA_databases/silva-arc-23s-id98.fasta -ref data/rRNA_databases/rfam-5s-database-id98.fasta -ref data/rRNA_databases/rfam-5.8s-database-id98.fasta -reads data/WHYR190420736_head_clean_1.fq.gz -reads data/WHYR190420736_head_clean_2.fq.gz --fastx --aligned WHYR190420736_head_clean_alligned --other --paired_in --num_alignments 1 -v -workdir run in /home/biosoft/sortmerna --out2
#按esc,输入：wq
# run
nohup ./sortrna.sh &
参考链接：sortmerna/README.md at master · biocore/sortmerna · GitHub
