Linux | parallel 并行2

1、使用gzip对 *.txt文件进行压缩

（1）parallel并行版本

ls *.txt | awk '{print "gzip "$1}' | parallel -j 3 {}
for file in `ls *txt` ; do echo gzip $file; done | parallel -j 3

（2）读取命令版本

ls *.txt | awk '{print "gzip "$1}' > gzip.sh
parallel -j 3 < gzip.sh
cat gzip.sh|parallel -j 4
parallel -j 3 --verbose --progress :::: gzip.sh

--verbose参数可以在执行命令语句前，先打印出该命令；
--progress参数可以实时显示任务的完成进度

解压

 for f in `ls ./*gz` ; do echo "name=`basename $f .gz`; gunzip -c $f >~/\$name"; done |parallel -j 2

2、批量 samtools flagstat

ls *bam
# SRR12720999.bam  SRR12721000.bam  SRR12721001.bam  

# 复杂命令(这里主要指>重定向符号)部分建议加上引号
parallel -j4 'samtools flagstat {} > {.}.stat' ::: *.bam

3、trim_galore

cat SraAccList.txt | while read id
do 
    echo $id
    echo trim_galore -j 8 -q 25 --phred33 --length 36 -paired -o trim \
        ${id}_1.fastq.gz \
        ${id}_2.fastq.gz >> parellel.txt
done


# 每次运行3条命令语句
parallel -j3 --verbose --progress :::: parellel.txt

https://blog.csdn.net/u014389734/article/details/80665849
https://blog.csdn.net/weixin_29602351/article/details/116863908
https://blog.csdn.net/weixin_29209805/article/details/116636181
https://blog.csdn.net/weixin_33349121/article/details/116713196

参考链接：
https://www.jianshu.com/p/cc54a72616a1
https://www.biostars.org/p/63816/
https://www.gnu.org/software/parallel/parallel_tutorial.html