# ### Bash-Oneliner
# Hi bash learners and bioinformaticans, welcome to Bash Oneliner. I started studying bioinformatics data three years ago (recently started working on cloud computing), and was amazed by those single-word bash commands which are much faster than my dull scripts, so i started bash. Not all the code here is oneliner (if the ';' counts..), but i put effort on making them brief and fast. 

# This blog will focus on simple bash commands for parsing data, most of which are for tsv files (tab-separated values); some of them are for Linux system maintenance. I apologize that there won't be any citation for the codes, but they are probably from dear Google and Stackoverflow.

# English and bash are not my first language, so... correct me anytime, thank you

# In case you would like to check and vote up my questions on Stackoverflow, here's my page:
# http://stackoverflow.com/users/4290753/once

# Here's a more stylish version of Bash-Oneliner~
# http://onceupon.github.io/Bash-Oneliner/

# ## Handy Bash oneliner commands for tsv file editing

# - [Grep](#grep)
# - [Sed](#sed)
# - [Awk](#awk)
# - [Xargs](#xargs)
# - [Find](#find)
# - [Loops](#loops)
# - [Math](#math)
# - [Download](#download)
# - [Random](#random)
# - [Xwindow](#xwindow)
# - [Others](#others)
# - [System](#system)

## Grep
#####  Extract text bewteen words (e.g. w1,w2)
    

grep -o -P '(?<=w1).*(?=w2)'


##### Grep lines without word (e.g. bbo)
     

grep -v bbo filename


##### Grep only one/first match (e.g. bbo)


grep -m 1 bbo filename


##### Grep and count (e.g. bbo)
    

grep -c bbo filename


##### Insensitive grep (e.g. bbo/BBO/Bbo)
    

grep -i "bbo" filename 


##### Count occurrence (e.g. three times a line count three times)
    

grep -o bbo filename 


##### COLOR the match (e.g. bbo)!
    

grep --color bbo filename 


##### Grep search all files in a directory(e.g. bbo)
    

grep -R bbo /path/to/directory 


# or
    

grep -r bbo /path/to/directory 

##### Search all files in directory, only output file names with matches(e.g. bbo)
    

grep -Rh bbo /path/to/directory 

# or
    
grep -rh bbo /path/to/directory 


##### Grep OR (e.g. A or B or C or D)
    

grep 'A\|B\|C\|D' 


##### Grep AND (e.g. A and B)
    

grep 'A.*B' 


##### Grep all content of a fileA from fileB
    

grep -f fileA fileB 


##### Grep a tab
    

grep $'\t' 


##### Grep variable from variable

$echo "$long_str"|grep -q "$short_str"
if [ $? -eq 0 ]; then echo 'found'; fi

# grep -q will output 0 if match found  
# remember to add space between []!

##### Grep strings between a bracket()

grep -oP '\(\K[^\)]+'


##### Grep number of characters with known strings in between(e.g. AAEL000001-RA)

grep -o -w "\w\{10\}\-R\w\{1\}"
  
# \w word character [0-9a-zA-Z_] \W not word character 


##### A lot examples here: http://www.cyberciti.biz/faq/grep-regular-expressions/



## Sed
##### Remove lines with word (e.g. bbo)
    

sed "/bbo/d" filename


##### Edit infile (edit and save)
    

sed -i "/bbo/d" filename

##### When using variable (e.g. $i), use double quotes " "
# e.g. add >$i to the first line (to make a FASTA file)  
    

sed "1i >$i"  

# notice the double quotes! in other examples, you can use a single quote, but here, no way!   
# '1i' means insert to first line


##### Delete empty lines
    

sed '/^\s*$/d' 
    
# or
   

sed 's/^$/d' 

##### Delete last line
   

sed '$d' 


##### Delete last character from end of file

sed -i '$ s/.$//' filename


##### Add string to end of file (e.g. "]")


sed '$s/$/]/' filename

##### Add newline to the end


sed '$a\'


##### Add string to beginning of every line (e.g. bbo)


sed -e 's/^/bbo/' file


##### Add string to end of each line (e.g. "}")

sed -e 's/$/\}\]/' filename


##### Add \n every nth character (e.g. every 4th character)
    

sed 's/.\{4\}/&\n/g' 


##### Concatenate/combine/join files with a seperator and next line (e.g seperate by ",")


sed -s '$a,' *.json > all.json


##### Substitution (e.g. replace A by B)
    

sed 's/A/B/g' filename 

##### Select lines start with string (e.g. bbo)
    

sed -n '/^@S/p' 

##### Delete lines with string (e.g. bbo)
    

sed '/bbo/d' filename 

##### Print every nth lines
    

sed -n '0~3p' filename

# catch 0: start; 3: step


##### Print every odd # lines
    

sed -n '1~2p' 

##### Print every third line including the first line
    

sed -n '1p;0~3p' 

##### Remove leading whitespace and tabs
    

sed -e 's/^[ \t]*//'

# notice a whitespace before '\t'!!


##### Remove only leading whitespace
    

sed 's/ *//'

# notice a whitespace before '*'!!


##### Remove ending commas
    

sed 's/,$//g' 

##### Add a column to the end
    

sed "s/$/\t$i/"

# $i is the valuable you want to add  
# e.g. add the filename to every last column of the file  
    

for i in $(ls);do sed -i "s/$/\t$i/" $i;done

##### Add extension of filename to last column


for i in T000086_1.02.n T000086_1.02.p;do sed "s/$/\t${i/*./}/" $i;done >T000086_1.02.np


##### Remove newline\ nextline
    

sed ':a;N;$!ba;s/\n//g'


##### Print a number of lines (e.g. line 10th to line 33 rd)
    

sed -n '10,33p' <filename


##### Change delimiter 

sed 's=/=\\/=g'


##### Replace with wildcard (e.g A-1-e or A-2-e or A-3-e....)

sed 's/A-.*-e//g' filename

##### Remove last character of file

sed '$ s/.$//'


##### Insert character at specified position of file (e.g. AAAAAA --> AAA#AAA)

sed -r -e 's/^.{3}/&#/' file



## Awk

##### Set tab as field separator
    

awk -F $'\t'  


##### Output as tab separated (also as field separator)
   

awk -v OFS='\t' 


##### Pass variable


a=bbo;b=obb;
awk -v a="$a" -v b="$b" "$1==a && $10=b" filename


##### Print line number and number of characters on each line
    

awk '{print NR,length($0);}' filename 


##### Find number of columns
  

awk '{print NF}' 


##### Reverse column order
    

awk '{print $2, $1}' 


##### Check if there is a comma in a column (e.g. column $1)
    

awk '$1~/,/ {print}'  


##### Split and do for loop
    

awk '{split($2, a,",");for (i in a) print $1"\t"a[i]}' filename 


##### Print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
    

awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'


##### Print filename and last line of all files in directory

ls|xargs -n1 -I file awk '{s=$0};END{print FILENAME,s}' file


##### Add string to the beginning of a column (e.g add "chr" to column $3)
    

awk 'BEGIN{OFS="\t"}$3="chr"$3' 


##### Remove lines with string (e.g. bbo)
    

awk '!/bbo/' file 


##### Column subtraction
    

cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'


##### Usage and meaning of NR and FNR
# e.g.  
# fileA:  
# a  
# b  
# c  
# fileB:  
# d  
# e  
    

awk 'print FILENAME, NR,FNR,$0}' fileA fileB 


# fileA    1    1    a  
# fileA    2    2    b  
# fileA    3    3    c  
# fileB    4    1    d  
# fileB    5    2    e  

##### AND gate

# e.g.  
# fileA:  
# 1    0  
# 2    1  
# 3    1  
# 4    0  

# fileB:  
# 1    0  
# 2    1  
# 3    0  
# 4    1  
    

awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB 


# 1    0  
# 2    1  
# 3    0  
# 4    0  

##### Round all numbers of file (e.g. 2 significant figure)
    

awk '{while (match($0, /[0-9]+\[0-9]+/)){
    \printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
    \$0=substr($0, RSTART+RLENGTH)
    \}
    \print
    \}'


##### Give number/index to every row
    

awk '{printf("%s\t%s\n",NR,$0)}'

##### Break combine column data into rows

# e.g.  
# seperate  

# David    cat,dog  
# into  
# David    cat  
# David    dog  

# detail here:　http://stackoverflow.com/questions/33408762/bash-turning-single-comma-separated-column-into-multi-line-string

awk '{split($2,a,",");for(i in a)print $1"\t"a[i]}' file


##### Sum up a file (each line in file contains only one number)


awk '{s+=$1} END {print s}' filename


##### Average a file (each line in file contains only one number)

awk '{s+=$1}END{print s/NR}'


##### Print field start with string (e.g Linux)


awk '$1 ~ /^Linux/'


##### Sort a row (e.g. 1 40  35  12  23  --> 1 12    23  35  40)


awk ' {split( $0, a, "\t" ); asort( a ); for( i = 1; i <= length(a); i++ ) printf( "%s\t", a[i] ); printf( "\n" ); }'


##### Subtract previous row values (add column6 which equal to column4 minus last column5) 

awk '{$6 = $4 - prev5; prev5 = $5; print;}'




## Xargs


##### Set tab as delimiter (default:space)


xargs -d\t


##### Display 3 items per line


echo 1 2 3 4 5 6| xargs -n 3


# 1 2 3  
# 4 5 6


##### Prompt before execution


echo a b c |xargs -p -n 3


##### Print command along with output


xargs -t abcd


# /bin/echo abcd  
# abcd


##### With find and rm


find . -name "*.html"|xargs rm -rf


##### Delete fiels with whitespace in filename (e.g. "hello 2001")


find . -name "*.c" -print0|xargs -0 rm -rf


##### Show limits


xargs --show-limits


##### Move files to folder


find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old


or


find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old


##### Move first 100th files to a directory (e.g. d1)


ls |head -100|xargs -I {} mv {} d1


##### Parallel


time echo {1..5} |xargs -n 1 -P 5 sleep

# a lot faster than

time echo {1..5} |xargs -n1 sleep


##### Copy all files from A to B


find /dir/to/A -type f -name "*.py" -print 0| xargs -0 -r -I file cp -v -p file --target-directory=/path/to/B


# v: verbose|  
# p: keep detail (e.g. owner)


##### With sed


ls |xargs -n1 -I file sed -i '/^Pos/d' filename


##### Add the file name to the first line of file


ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt


##### Count all files


ls |xargs -n1 wc -l


##### Turn output into a single line


ls -l| xargs


##### Count files within directories


echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' --

 # "--" signals the end of options and display further option processing


##### Download dependencies files and install (e.g. requirements.txt)
 

cat requirements.txt| xargs -n1 sudo pip install


##### Count lines in all file, also count total lines


ls|xargs wc -l

##### Xargs and grep


cat grep_list |xargs -I{} grep {} filename


## Find 

##### List all sub directory/file in the current directory
    

find .


##### List all files under the current directory
    

find . -type f


##### List all directories under the current directory
    

find . -type d


##### Edit all files under current directory (e.g. replace 'www' with 'ww')
    

find . name '*.php' -exec sed -i 's/www/w/g' {} \;

# if no subdirectory
    

replace "www" "w" -- *

# a space before *


##### Find and output only filename (e.g. "mso")
    

find mso*/ -name M* -printf "%f\n"


##### Find and delete file with size less than (e.g. 74 byte)
    

find . -name "*.mso" -size -74c -delete

# M for MB, etc


## Loops

##### While loop, column subtraction of a file (e.g. a 3 columns file)
    

while read a b c; do echo $(($c-$b));done < <(head filename)

# there is a space between the two '<'s

##### While loop, sum up column subtraction
    

i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)


##### If loop
    

if (($j==$u+2))

# (( )) use for arithmetic operation
    

if [[$age >21]]

# [[ ]] use for comparison


##### Test if file exist

if [ -e 'filename' ]
then
  echo -e "file exists!"
fi



##### For loop
    

for i in $(ls); do echo file $i;done


## Math

##### Print out the prime factors of a number (e.g. 50)

factor 50


##### Simple math with expr

expr 10+20 #30
expr 10\*20 #600
expr 30 \> 20 #1 (true)


##### More math with bc

# - Number of decimal digit/ significant figure  

echo "scale=2;2/3" | bc  
#.66

# - Exponent operator  

echo "10^2" | bc  
#100


# - Using variables   

echo "var=5;--var"| bc  
#4




## Download

##### Download all from a page
    

wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com

# -r: recursive and download all links on page  
# -l1: only one level link  
# -H: span host, visit other hosts  
# -t1: numbers of retries  
# -nd: don't make new directories, download to here  
# -N: turn on timestamp  
# -nd: no parent  
# -A: type (seperate by ,)  
# -e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com  

##### Upload a file to web and download (https://transfer.sh/)
# --> upload:

curl --upload-file ./filename.txt https://transfer.sh/filename.txt

# (the above command will return a URL, e.g: https://transfer.sh/tG8rM/filename.txt)  
# --> download:

curl https://transfer.sh/tG8rM/filename.txt -o filename.txt



##### Download file if necessary
    

data=file.txt
url=http://www.example.com/$data
if [! -s $data];then
    echo "downloading test data..."
    wget $url
fi


##### Wget to a filename (when a long name)
    

wget -O filename "http://example.com"


##### Wget files to a folder


wget -P /path/to/directory "http://example.com"



## Random
##### Random pick 100 lines from a file
    

shuf -n 100 filename


##### Random order (lucky draw)
    

for i in a b c d e; do echo $i; done| shuf


##### Echo series of random numbers between a range (e.g. shuffle numbers from 0-100, then pick 15 of them randomly)
    

shuf -i 0-100 -n 15


##### Echo a random number
    

echo $RANDOM


##### Random from 0-9
    

echo $((RANDOM % 10))


##### Random from 1-10
    

echo $(((RANDOM %10)+1))


## Xwindow
# X11 GUI applications! Here are some GUI tools for you if you get bored by the text-only environment.  


##### Enable X11 forwarding,in order to use graphical application on servers

ssh -X user_name@ip_address

# or setting through xhost

# --> Install the following for Centos:  
# xorg-x11-xauth  
# xorg-x11-fonts-*  
# xorg-x11-utils  

##### Little xwindow tools
    

xclock
xeyes
xcowsay


##### Open pictures/images from ssh server

# 1. ssh -X user_name@ip_address
# 2. apt-get install eog
# 3. eog picture.png


##### Use gedit on server (GUI editor) 

# 1. ssh -X user_name@ip_address
# 2. apt-get install gedit
# 3. gedit filename.txt

##### Open PDF file from ssh server 

# 1. ssh -X user_name@ip_address
# 2. apt-get install evince
# 3. evince filename.pdf

##### Use google-chrome browser from ssh server 

# 1. ssh -X user_name@ip_address
# 2. apt-get install libxss1 libappindicator1 libindicator7
# 3. wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
# 4. sudo apt-get install -f
# 5. dpkg -i google-chrome*.deb
# 6. google-chrome
 




## Others

##### Remove newline / nextline
    

tr --delete '\n' <input.txt >output.txt


##### Replace newline
     

tr '\n' ' ' <filename


##### To uppercase/lowercase
     

tr /a-z/ /A-Z/


##### Compare files (e.g. fileA, fileB)
    

diff fileA fileB

# a: added; d:delete; c:changed

# or


sdiff fileA fileB

# side-to-side merge of file differences


##### Number a file (e.g. fileA)


nl fileA

# or


nl -nrz fileA

# add leading zeros


##### Combine/ paste two files (e.g. fileA, fileB)
    

paste fileA fileB

# default tab seperated


##### Reverse string
    

echo 12345| rev


##### Read .gz file without extracting
    

zmore filename

# or
    

zless filename


##### Run in background, output error file
    

seq 100  &>log &


# or



seq 100 2>log &


# or


seq 100 2>&1| tee logfile


# or


seq 100 2>&1 >>outfile

# 0: standard input; 1: standard output; 2: standard error


##### Send mail
    

echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com

# use -a flag to set send from (-a "From: some@mail.tld")


##### .xls to csv
    

xls2csv filename

##### Append to file (e.g. hihi)
    

echo 'hihi' >>filename


##### Make BEEP sound
    

speaker-test -t sine -f 1000 -l1


##### Set beep duration
    

(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid


##### History edit/ delete
    

~/.bash_history

# or


history -d [line_number]


##### Get last history/record filename
    

head !$


##### Clean screen
    

clear


# or


Ctrl+l


##### Send data to last edited file
    

cat /directory/to/file
echo 100>!$


##### Run history number (e.g. 53)
    

!53


##### Run last command
    

!!


##### Run last command that began with (e.g. cat filename)
    

!cat


or


!c

# run cat filename again


##### Extract .xf
    
    1.unxz filename.tar.xz  
    2.tar -xf filename.tar

##### Install python package
    

pip install packagename


##### Delete current bash command
    

Ctrl+U


# or


Ctrl+C


# or


Alt+Shift+#

# to make it to history


##### Add something to history (e.g. "addmetohistory")
    

#addmetodistory

# just add a "#" before~~


##### Sleep awhile or wait for a moment or schedule a job
    

sleep 5;echo hi


##### Count the time for executing a command
    

time echo hi


##### Backup with rsync
    

rsync -av filename filename.bak
rsync -av directory directory.bak
rsync -av --ignore_existing directory/ directory.bak
rsync -av --update directory directory.bak
rsync -av directory user@ip_address:/path/to/directory.bak

# skip files that are newer on receiver (i prefer this one!)


##### Make all directories at one time!
    

mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat}

# -p: make parent directory  
# this will create project/doc/html/; project/doc/info; project/lib/ext ,etc


##### Run command only if another command returns zero exit status (well done)
    

cd tmp/ && tar xvf ~/a.tar


##### Run command only if another command returns non-zero exit status (not finish)
    

cd tmp/a/b/c ||mkdir -p tmp/a/b/c


##### Extract to a path
    

tar xvf -C /path/to/directory filename.gz


##### Use backslash "\" to break long command
    

cd tmp/a/b/c \
> || \
>mkdir -p tmp/a/b/c


##### Get pwd
    

VAR=$PWD; cd ~; tar xvf -C $VAR file.tar

# PWD need to be capital letter

##### List file type of file (e.g. /tmp/)
    

file /tmp/

# tmp/: directory


##### Bash script
    

#!/bin/bash
file=${1#*.}

# remove string before a "."


file=${1%.*}

# remove string after a "."

##### Search from history
    

Ctrl+r


##### Python simple HTTP Server
    

python -m SimpleHTTPServer


##### Variables
    

{i/a/,}

# e.g. replace all

{i//a/,}

# for variable i, replace all 'a' with a comma

##### Read user input
    

read input
echo $input


##### Generate sequence 1-10
    

seq 10


##### Sum up input list (e.g. seq 10)
    

seq 10|paste -sd+|bc


##### Find average of input list/file
    

i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc


##### Generate all combination (e.g. 1,2)
    

echo {1,2}{1,2}

# 1 1, 1 2, 2 1, 2 2

##### Generate all combination (e.g. A,T,C,G)
    

set = {A,T,C,G}
group= 5
for ((i=0; i<$group; i++));do
    repetition=$set$repetition;done
    bash -c "echo "$repetition""


##### Read file content to variable

foo=$(<test1)


##### Echo size of variable


echo ${#foo}


##### Echo tab


echo -e ' \t '


##### Array

declare -A array=()


##### Send a directory


scp -r directoryname user@ip:/path/to/send


##### Split file into lines (e.g. 1000 lines/smallfile)

split -d -l 1000 bigfilename


##### Rename all files (e.g. remove ABC from all .gz files)

rename 's/ABC//' *.gz


##### Remove extention (e.g remove .gz from filename.gz)

basename filename.gz .gz

zcat filename.gz> $(basename filename.gz .gz).unpacked


##### Use the squeeze repeat option (e.g. /t/t --> /t)

tr -s "/t" < filename


##### Do not print nextline with echo

echo -e 'text here \c'


##### Use the last argument

!$


##### Check last exit code

echo $?

##### View first 50 characters of file

head -c 50 file

 
##### Group/combine rows into one row 

# e.g.  
# AAAA  
# BBBB  
# CCCC  
# DDDD  

cat filename|paste - -
# -->
# AAAABBBB
# CCCCDDDD
cat filename|paste - - - -
# -->
# AAAABBBBCCCCDDDD


##### Fastq to fasta 

cat file.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' >file.fa

##### Cut and get last column

cat file|rev | cut -d/ -f1 | rev


##### Add one to variable/increment a numeric variable (e.g. $var)

((var++))


##### Some handy environment variables
# $0   :name of shell or shell script.  
# $1, $2, $3, ... :positional parameters.  
# $#   :number of positional parameters.  
# $?   :most recent foreground pipeline exit status.  
# $-   :current options set for the shell.  
# $$   :pid of the current shell (not subshell).  
# $!   :is the PID of the most recent background command.  

##### Clear the contents of a file (e.g. filename)

>filename

##### Unzip tar.bz2 file (e.g. file.tar.bz2)

tar xvfj file.tar.bz2

##### Output a y/n repeatedly until killed 
# 'y':

yes

# or 'n':

yes n

# or 'anything':

yes anything


# For example: 

yes | rm -r large_directory
 

##### Create dummy file of certain size instantly (e.g. 200mb)

dd if=/dev/zero of=//dev/shm/200m bs=1024k count=200
 

# Standard output:  
# 200+0 records in  
# 200+0 records out  
# 209715200 bytes (210 MB) copied, 0.0955679 s, 2.2 GB/s  

##### Cat to a file

cat >myfile
let me add sth here
exit by control + c
^C
 

##### Keep /repeatedly executing the same command (e.g Repeat 'wc -l filename' every 1 second)

watch -n 1 wc -l filename
 

##### Print commands and their arguments when execute (e.g. echo `expr 10 + 20 `)

set -x; echo `expr 10 + 20 `
 

##### Print some meaningful sentences to you (install fortune first)

fortune
 
##### Colorful (and useful) version of top (install htop first)

htop
 

## System

##### Snapshot of the current processes


ps 


##### Check graphics card


lspci


##### Show IP address
    

$ip add show

or
    

ifconfig


##### Check system version
    

cat /etc/*-release


##### Linux Programmer's Manuel: hier- description of the filesystem hierarchy
    

man hier


##### List job
    

jobs -l


##### Export PATH
    

export PATH=$PATH:~/path/you/want


##### Make file execuable
    

chmod +x filename

# you can now ./filename to execute it

##### List screen
    

screen -d -r


##### Echo screen name
    

screen -ls


##### Check system (x86-64)
    

uname -i


##### Surf the net


links www.google.com


##### Add user, set passwd
    

useradd username
passwd username


##### Edit variable for bash, (e.g. displaying the whole path)
    

# 1. joe ~/.bash_profile 
# 2. export PS1='\u@\h:\w\$' 

# $PS1 is a variable that defines the makeup and style of the command prompt 

# 3. source ~/.bash_profile


##### Edit environment setting (e.g. alias)
    

# 1. joe ~/.bash_profile
# 2. alias pd="pwd" //no more need to type that 'w'!
# 3. source ~/.bash_profile


##### List environment variables (e.g. PATH)
    

$echo $PATH

# list of directories separated by a colon

##### List all environment variables for current user
    

$env


##### Show partition format
    

lsblk


##### Soft link program to bin
    

ln -s /path/to/program /home/usr/bin

# must be the whole path to the program

##### Show hexadecimal view of data
    

hexdump -C filename.class


##### Jump to different node
    

rsh node_name


##### Check port (active internet connection)
    

netstat -tulpn


##### Find whick link to a file
    

readlink filename


##### Check where a command link to (e.g. python)
    

which python


##### List total size of a directory
    

du -hs .

or
    

du -sb


##### Copy directory with permission setting
    

cp -rp /path/to/directory


##### Store current directory
    

pushd . $popd ;dirs -l 


##### Show disk usage
    

df -h 

# or
   

du -h 

# or
    

du -sk /var/log/* |sort -rn |head -10


##### Show current runlevel
    

runlevel


##### Switch runlevel
    

init 3 

# or

telinit 3 

##### Permanently modify runlevel
    

1. edit /etc/init/rc-sysinit.conf 
2. env DEFAULT_RUNLEVEL=2 


##### Become root
    

su


##### Become somebody
    

su somebody


##### Report user quotes on device
    

requota -auvs


##### Get entries in a number of important databases
    

getent database_name

# (e.g. the 'passwd' database)
    

getent passwd

# list all user account (all local and LDAP)  
# (e.g. fetch list of grop accounts)
    

getent group

# store in database 'group'

##### Change owner of file
    

chown user_name filename
chown -R user_name /path/to/directory/

# chown user:group filename

##### List current mount detail
    

df


##### List current usernames and user-numbers
    

cat /etc/passwd

##### Get all username
    

getent passwd| awk '{FS="[:]"; print $1}'


##### Show all users
    

compgen -u


##### Show all groups
    

compgen -g


##### Show group of user
    

group username


##### Show uid, gid, group of user
    

id username


##### Check if it's root
    

if [$(id -u) -ne 0];then
    echo "You are not root!"
    exit;
fi

# 'id -u' output 0 if it's not root

##### Find out CPU information
    

more /proc/cpuinfo

# or
    

lscpu


##### Set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120)
    

setquota username 120586240 125829120 0 0 /home


##### Show quota for user
    

quota -v username


##### Fork bomb
    

# :(){:|:&};:

# dont try this at home

##### Check user login
    

lastlog


##### Edit path for all users
    

joe /etc/environment

# edit this file

##### Show running processes
    

ps aux


##### Find maximum number of processes
    

cat /proc/sys/kernal/pid_max


##### Show and set user limit
    

ulimit -u

##### Which ports are listening for TCP connections from the network


nmap -sT -O localhost


##### Print out number of cores/ processors


nproc --all

##### Check status of each core
# 1. top  
# 2. press '1'

##### Show jobs and PID


jobs -l


##### List all running services


service --status-all


##### Schedule shutdown server

shutdown -r +5 "Server will restart in 5 minutes. Please save your work."

##### Cancel scheduled shutdown

shutdown -c


##### Boardcast to all users

wall -n hihi

##### Kill all process of a user

pkill -U user_name

##### Set gedit preference on server

# -->you might have to install the following:

apt-get install libglib2.0-bin;  

yum install dconf dconf-editor;  
yum install dbus dbus-x11;  

# -->Check list  

gsettings list-recursively

# -->Change setting  
# e.g.

gsettings set org.gnome.gedit.preferences.editor highlight-current-line true
gsettings set org.gnome.gedit.preferences.editor scheme 'cobalt'
gsettings set org.gnome.gedit.preferences.editor use-default-font false
gsettings set org.gnome.gedit.preferences.editor editor-font 'Cantarell Regular 12'

##### Find out who has logged in on your system
--> [Quick] Printing out only the names:

users


# --> [Detail] Printing out login time, load average, etc

w

##### Add user to a group (e.g add user 'nice' to the group 'docker', so that he can run docker without sudo) 

sudo gpasswd -a nice docker


##### pip install python package without root 

# 1. pip install --user package_name
# 2. You might need to export ~/.local/bin/ to PATH: export PATH=$PATH:~/.local/bin/


##### Removing old linux kernels (when /boot almost full...)

# 1. uname -a  #check current kernel, which should NOT be removed
# 2. sudo apt-get purge linux-image-X.X.X-X-generic  #replace old version



##### Change hostname

sudo hostname your-new-name

# if not working, do also:  

hostnamectl set-hostname your-new-hostname

then run:  
hostnamectl

# check /etc/hostname  

# if still not working..., edit:  
# /etc/sysconfig/network  
# /etc/sysconfig/network-scripts/ifcfg-ensxxx  
# add HOSTNAME="your-new-hostname"  
  

##### List installed packages

apt list --installed

# or Red Hat: 

yum list installed

##### Tutorial for setting up your own DNS server
# http://onceuponmine.blogspot.tw/2017/08/set-up-your-own-dns-server.html

##### Tutorial for creating a simple daemon
# http://onceuponmine.blogspot.tw/2017/07/create-your-first-simple-daemon.html



# =-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-