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              v 0.0.1

About

Cycle.sh is a small bash script to auto-run the custom commands with looping in folders in linux-like system.

Install

1.download this project:

git clone

2. install 3rd_partylib with run install_3rd.sh

./Cycle/3rd_partylib/./install_3rd.sh

3. add your path to Cycle to $PATH , for example :

using vim open ~/.bashrc

sudo vim ~/.bashrc

edit .bashrc , add the path :

PATH=~/Cycle/:$PATH

source ~/.bashrc

Usage

./cycle.sh

-i input root path

-o output root path

-p output postfix ,defult is 'result'

-a input folder prefix

-b input folder postfix for input

(search folder pattern as a*b , defult is all)

-n not creat output sub folder , defult will creat by mkdir command

use

Define custom commands

please use those two var :

$input_sub_dir , the root of input folder for each loop

$output_each_dir, the output folder for each loop

to define the commands your own , for example:

custom_cmd.sh:

cmd='ls $input_sub_dir > $output_each_dir/data.txt &'
echo "run cmd : "$cmd
eval $cmd

and run :

./cycle.sh -i ./test -o ./out -c custom_cmd.sh

the outputs will be like:


current procressing input dir : ./test/1
current output dir : ./out/1_result
run cmd : ls $input_sub_dir > $output_each_dir/data.txt &
-----------------------
current procressing input dir : ./test/2
current output dir : ./out/2_result
run cmd : ls $input_sub_dir > $output_each_dir/data.txt &
-----------------------
current procressing input dir : ./test/3
current output dir : ./out/3_result
run cmd : ls $input_sub_dir > $output_each_dir/data.txt &
-----------------------

The input path structure:

Cycle/test
├── 1
│   └── 1.txt
├── 2
│   └── 2.txt
└── 3
    └── 3.txt

3 directories, 3 files

The output path structure:

/Cycle/out
├── 1_result
│   └── data.txt
├── 2_result
│   └── data.txt
└── 3_result
    └── data.txt

3 directories, 3 files

Application example for looping fastqc

1. load data from fastq-dump

./test_2/./load_data.s

2. creat command file custom_cmd2.sh:

fastqc -t 16 -o $output_each_dir $input_sub_dir/fastq

3. run Cycle.sh

./cycle.sh -i ./test_2 -o ./out_2 -c custom_cmd2.sh -p fastqc -a SRR

result will be

├── SRR650259_fastqc
│   ├── fastq_fastqc.html
│   └── fastq_fastqc.zip
├── SRR650290_fastqc
│   ├── fastq_fastqc.html
│   └── fastq_fastqc.zip
├── SRR651263_fastqc
│   ├── fastq_fastqc.html
│   └── fastq_fastqc.zip
├── SRR651328_fastqc
│   ├── fastq_fastqc.html
│   └── fastq_fastqc.zip
└── SRR651357_fastqc
    ├── fastq_fastqc.html
    └── fastq_fastqc.zip

whuang022ai/Cycle