3.Bash and Github

How to set up multiple jobs as a pipeline

1) Github

(1) Desktop Version for Mac or Windows

I downloaded the desktop version of github on mac.

(2) Terminal Version for Linux or Mac

Setup:

1) add a setting file:

~/.gitconfig:

[user] 
email =[[e-mail]]
name = Shared

2) Copy your ssh key to github website (set up ssh key) 3) Add a repository in github website

Clone a repository:

git clone [e-mail]:lulab/RNAfinder_Server.git

Add:

git add exmaples/
git commit -a
git push origin

Change:

git commit -a
git push origin

Remove:

git rm *.file
git commit -a
git push origin
git pull?

Pull (update):

git pull origin master
git log -n 2 # look at the last two log entries.

more

Case study: how to use google to solve question

• Q1: How to install terminal version of git in mac?

• A1: google "install git _on _mac" --> I got the answer

• Q2: After I installed git, I got such error:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun"

• A2: google this whole sentence --> I got the answer

2) Bash Examples

Example I

install software and tools in a brand-new OS

(1) 安装vim

yum -y install vim

(2) 打开一个空shell文件

vim myinstall.sh

(3) 复制如下shell脚本到smyinstall.sh内。此shell文件会自动安装包括：R-2.15.3，perl-5.26.1等

yum -y install wget
yum -y install readline-devel
yum -y install libXt-devel
yum -y install gcc gcc-c++
yum -y install gcc-gfortran
yum -y install libg2c.so.0
yum -y install less
yum -y install bzip2-devel
yum -y install zlib-devel
yum -y install xz-devel.x86_64
yum -y install make
yum -y install zip unzip

mkdir /download
cd /download
wget -c http://www.cpan.org/src/5.0/perl-5.26.1.tar.gz
tar -xvzf perl-5.26.1.tar.gz
cd /download/perl-5.26.1
sh Configure -de
make
make test
make install

(4) 执行shell脚本

bash myinstall.sh > myinstall.log    # Standard output to a log file
bash myinstall.sh >& myinstall.log   # Log both Standard output and Standard error
bash myinstall.sh > myinstall.log  2> myinstall.err # Log STDOUT and STDERR separately

Example II

backup files using rsync and crontab

(0) install rsync and crontab

yum -y install rsync
yum -y install crontabs

mkdir /mac/backup   # prepare the backup dir

(1) Prepare a backup script, for example, "~/backup.sh"

#!/bin/bash

#1. Local backup  
RSYNC="rsync --stats  --compress --recursive --times --perms --links --delete --max-size=100M --exclude-from=/home/john/.rsync/exclude"

echo "1. Backup of /home/john start at:"
date
$RSYNC /home/john/data/  /mac/backup/
echo "Backup end at:"
date



#2. Remote backup 
RSYNC="rsync --stats  --compress --recursive --times --perms --links --delete --max-size=100M"

echo "2. Backup 172.22.220.20:/data/ to /mac/backup2/ start at:"
date
$RSYNC john@172.22.220.20:/home/john/data/ /mac/backup2/
echo "Backup end at:"
date

(2) Using "crontab" command to execute the backup script routinely, and record in a log file, for example,

execute the command "~/backup.sh > ~/backup.log" in 5:10am everyday:

chmod +x ~/backup.sh

1) open crontab and edit it by the following command: 

crontab -e  or crontab ~/cronjob

2) type in the following lines or write the following in a file (i.e. ~/crontab): 

# minute hour day_in_month month day_in_week command
     10   5  * * *   ~/backup.sh > ~/backup.log 

3) exit and save (like in VIM)

3) Tips

• awk

  gawk '{print $2 $1}' FILE | head -100
  cat FILE | gawk '(NR>2) {print }'
  
  gawk -f FILE # take command from file
  
    Begin { a=1; ORS = " "}  # ORS: output record seperator
    ...

• input STANDIN in your script

rnatotal.o <<EOF
trna.lis
trna.out
trna
EOF

• grep non ATGC nucleotides in fasta file

grep -v "^>" test.fasta | \    # ^ means start with here
grep --color -i "[^ATCG]"      # ^ means non- here

• A tee in your pipe

program1 input.txt | tee intermediate-file.txt | program2 > results.txt

• Exit Status

program1 input.txt > inter.txt && \   # run program 2 only if program1 is success (i.e. exit status is 0: $? = 0)
program2 inter.txt> results.txt

program1 input.txt > inter.txt || \
echo "warning: an error occurred

• Name dir with today's date

mkdir results-$(date +F%)  # +F% format is 2018-03-18

alias today="date +F%"  # you can put this in ~/.bashrc
mkdir results-$(today)

4）More Readings and Practices

• Teaching Video：Week II. 3. Bash

• for Beginners

阅读和练习《鸟哥的Linux私房菜-基础学习篇》如下章节:

第11章 认识与学习bash 第12章 正则表达式与文件格式化处理 第13章 学习shell script

• for Advanced Readers

  • More Bash Examples at Github

  • Additional Tutorial: Bash

  • <<Bioinformatics Data Skills>>

    • 5) Git for Scientists

    • 6) Bioinformatics Data

    • 12) Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks

5）Homework

1. 利用google等工具找到如何让awk读输入文件时只按照tab来做separator？

2. 学习和完成这里面的作业：Additional Tutorial : Bash (Teaching Video：Week II. Bash and R -- Shared by Li)

6) Video

6a) Bash and Github

@Youtube

@Bilibili