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README.md

Bash-Oneliner

I am glad that you are here! I started working on bioinformatics four years ago (recently switched to cloud computing), and was amazed by those single-word bash commands which are much faster than my dull scripts, so much time can be saved through knowing command-line shortcuts and scripting. Not all the code here is oneliner (if the ';' counts..), but i put effort on making them brief and fast. I am mainly using Ubuntu, RedHat and Linux Mint, sorry if the commands dont work on your system.

This blog will focus on simple bash commands for parsing data; some of them are for Linux system maintenance i acquired from work and when i was studying LPIC (I have LPIC1 certificate now ^^). I apologize that there are no detailed citation for all the commands, but they are probably from dear Google and Stackoverflow.

English and bash are not my first language, so... correct me anytime, thank you!
And if you know any cool command that are not included here, Please Teach Me.

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

Terminal Tricks
Variable
Grep
Sed
Awk
Xargs
Find
Loops
Math
Time
Download
Random
Xwindow
System
Hardware
Others

Terminal Tricks

Ctrl

Ctrl + n : same as Down arrow.
Ctrl + p : same as Up arrow.
Ctrl + r : begins a backward search through cammand history.(keep pressing Ctrl + r to move backward)
Ctrl + s : to stop output to terminal.
Ctrl + q : to resume output to terminal after Ctrl + s.
Ctrl + a : move to the beginning of line.
Ctrl + e : move to the end of line.
Ctrl + d : if you've type something, Ctrl + d deletes the character under the cursor, else, it escapes the current shell.
Ctrl + k : delete all text from the cursor to the end of line.
Ctrl + x + backspace : delete all text from the beginning of line to the cursor.
Ctrl + t : transpose the character before the cursor with the one under the cursor, press Esc + t to transposes the two words before the cursor.
Ctrl + x + Ctrl + e : launch editor define by $EDITOR

Change case

Esc + u
# converts text from cursor to the end of the word to uppercase.  
Esc + l
# converts text from cursor to the end of the word to uppercase. 
Esc + c
# converts letter under the cursor to uppercase.

Run history number (e.g. 53)

!53

Run last command

!!

Run last command and change some parameter (e.g. last command: echo 'aaa' -> rerun as: echo 'bbb')

#last command: echo 'aaa'
^aaa^bbb

#echo 'bbb'
#bbb

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

!cat

!c
# run cat filename again

Grep

[back to top]

Type of grep

grep = grep -G # Basic Regular Expression (BRE)
fgrep = grep -F # fixed text, ignoring meta-charachetrs
egrep = grep -E # Extended Regular Expression (ERE)
pgrep = grep -P # Perl Compatible Regular Expressions (PCRE)
rgrep = grep -r # recursive

Grep and return only integer

grep -o '[0-9]*'
#or
grep -oP '\d'

Grep integer with certain number of digits (e.g. 3)

grep ‘[0-9]\{3\}’
# or
grep -E ‘[0-9]{3}’
# or
grep -P ‘\d{3}’

Grep only IP address

grep -Eo '[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}'
# or
grep -Po '\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}'

Grep whole word (e.g. 'target')

grep -w 'target'
 
#or using RE
grep '\btarget\b'

Grep returning lines before and after match (e.g. 'bbo')

# return also 3 lines after match
grep -A 3 'bbo'
 
# return also 3 lines before match
grep -B 3 'bbo'

# return also 3 lines before and after match
grep -C 3 'bbo'

Grep string starting with (e.g. 'S')

grep -o 'S.*'

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 lines not begin with string (e.g. #)

grep -v '^#' file.txt

Grep variables with space within it (e.g. bbo="some strings")

grep "$boo" filename

#remember to quote the variable!

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

grep -m 1 bbo filename

Grep and return number of matching line(e.g. bbo)

grep -c bbo filename

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

grep -o bbo filename |wc -l

Case insensitive grep (e.g. bbo/BBO/Bbo)

grep -i "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

grep -r bbo /path/to/directory

Search all files in directory, do not ouput the filenames (e.g. bbo)

grep -rh bbo /path/to/directory

Search all files in directory, output ONLY the filenames with matches(e.g. bbo)

grep -rl 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'

Regex any singer character (e.g. ACB or AEB)

grep 'A.B'

Regex with or without a certain character (e.g. color or colour)

grep ‘colou?r’

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

Skip directory (e.g. bbo)

grep -d skip 'bbo' /path/to/files/*

Sed

[back to top]

Remove the 1st line

sed 1d filename

Remove the first 100 lines (remove line 1-100)

sed 1,100d filename

Remove lines with string (e.g. bbo)

sed "/bbo/d" filename
- case insensitive:
sed "/bbo/Id" filename

Remove lines whose nth character not equal to a value (e.g. 5th character not equal to 2)

sed -E '/^.{5}[^2]/d'
#aaaa2aaa (you can stay)
#aaaa1aaa (delete!)

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/remove empty lines

sed '/^\s*$/d'

sed '/^$/d'

Delete/remove last line

sed '$d'

Delete/remove last character from end of file

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

Add string to beginning of file (e.g. "[")

sed -i '1s/^/[/' file

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

Substitution with wildcard (e.g. replace a line start with aaa= by aaa=/my/new/path)

sed "s/aaa=.*/aaa=\/my\/new\/path/g"

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

sed -n '/^@S/p'

Delete lines with string (e.g. bbo)

sed '/bbo/d' filename

Print/get/trim a range of line (e.g. line 500-5000)

sed -n 500,5000p 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 particular line (e.g. 123th line)

sed -n -e '123p'

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

[back to top]

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

Remove last column

awk 'NF{NF-=1};1' file

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

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

[back to top]

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
 
# when using a backtick
rm `find . -name "*.html"`

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

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

Xargs and sed (replace all old ip address with new ip address under /etc directory)

grep -rl '192.168.1.111' /etc | xargs sed -i 's/192.168.1.111/192.168.2.111/g'

Find

[back to top]

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

[back to top]

If loop

# if and else loop for string matching
if [[ "$c" == "read" ]]; then outputdir="seq"; else outputdir="write" ; fi  

# Test if myfile contains the string 'test':
if grep -q hello myfile; then …

# Test if mydir is a directory, change to it and do other stuff:
if cd mydir; then
  echo 'some content' >myfile
else
  echo >&2 "Fatal error. This script requires mydir."
fi

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

# Test if file exist but also including symbolic links:
if [ -e myfile ] || [ -L myfile ]
then
  echo -e "file exists!"
fi

# Test if the value of x is greater or equal than 5
if [ "$x" -ge 5 ]; then …

# Test if the value of x is greater or equal than 5, in bash/ksh/zsh:
if ((x >= 5)); then …

# Use (( )) for arithmetic operation
if (($j==$u+2))

# Use [[ ]] for comparison
if [[$age >21]]

For loop

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

# Press any key to continue each loop
for i in $(cat tpc_stats_0925.log |grep failed|grep -o '\query\w\{1,2\}');do cat ${i}.log; read -rsp $'Press any key to continue...\n' -n1 key;done

# Print a file line by line when a key is pressed
for line in $(cat myfile); do echo $line; read -n1; done

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

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

# Keep checking a running process (e.g. perl) and start another new process (e.g. python) immetiately after it. (BETTER use the wait command! Ctrl+F 'wait')
while [[ $(pidof perl) ]];do echo f;sleep 10;done && python timetorunpython.py

switch (case in bash)

read type;
case $type in
  '0')
    echo 'how'
    ;;
  '1')
    echo 'are'
    ;;
  '2')
    echo 'you'
    ;;
esac

Variable

[back to top]

variable substitution within quotes

# foo=bar
 echo "'$foo'"
#'bar'
# double/single quotes around single quotes make the inner single quotes expand variables

get the length of variable

var="some string"
echo ${#var}  
# 11

get the first character of the variable

var="some string"
echo ${var%%"${var#?}"}
#s

remove the first or last string from variable

var="some string"
echo ${var:2}
#me string

replacement (e.g. remove the first leading 0 )

var="0050"
echo ${var[@]#0}
#050

replacement (e.g. replace 'a' with ',')

{var/a/,}

replace all (e.g. replace all 'a' with ',')

{var//a/,}

#with grep
 test="god the father"
 grep ${test// /\\\|} file.txt
 # turning the space into 'or' (\|) in grep

To change the case of the string stored in the variable to lower case (Parameter Expansion)

var=HelloWorld
echo ${var,,}
helloworld

Math

[back to top]

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

factor 50

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

seq 10|paste -sd+|bc

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

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

Column subtraction

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

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

Time

[back to top]

Find out the time require for executing a command

time echo hi

Wait for some time (e.g 10s)

sleep 10

Log out your account after a certain period of time (e.g 10 seconds)

TMOUT=10
#once you set this variable, logout timer start running!

Set how long you want to run a command

#This will run the commmand 'sleep 10' for only 1 second.
timeout 1 sleep 10

Set when you want to run a command (e.g 1 min from now)

at now + 1min  #time-units can be minutes, hours, days, or weeks
warning: commands will be executed using /bin/sh
at> echo hihigithub >~/itworks
at> <EOT>   # press Ctrl + D to exit
job 1 at Wed Apr 18 11:16:00 2018

Download

[back to top]

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

[back to top]

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

[back to top]

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

System

[back to top]

Snapshot of the current processes

ps

Check graphics card

lspci

Show IP address

$ip add show

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

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

Unset environment variable (e.g. unset variable 'MYVAR')

unset MYVAR

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 which 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 .

du -sb

Copy directory with permission setting

cp -rp /path/to/directory

Store current directory

pushd . $popd ;dirs -l

Show disk usage

df -h

du -h

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

Show current runlevel

runlevel

Switch runlevel

init 3

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

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

:(){:|:&};:

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
#notice that some commpanies might not like you using nmap

Print out number of cores/ processors

nproc --all

Check status of each core

top
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

Kill all process of a program

kill -9 $(ps aux | grep 'program_name' | awk '{print $2}')

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'

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

Check which file make the device busy on umount

lsof /mnt/dir

When sound not working

killall pulseaudio

then press Alt-F2 and type in pulseaudio

When sound not working

killall pulseaudio

List information about SCSI devices

lsscsi

Using telnet to test open ports, test if you can connect to a port (e.g 53) of a server (e.g 192.168.2.106)

telnet 192.168.2.106 53

change network maximum transmission unit (mtu) (e.g. change to 9000)

ifconfig eth0 mtu 9000

get pid of a running process (e.g python)

pidof python

ps aux|grep python

ntp

start ntp:

ntpd

check ntp:

ntpq -p

remove unnecessary files to clean your server

sudo apt-get autoremove
sudo apt-get clean
sudo rm -rf ~/.cache/thumbnails/*

Remove old kernal:

sudo dpkg --list 'linux-image*'
sudo apt-get remove linux-image-OLDER_VERSION

Increase/ resize root partition (root partition is an LVM logical volume)

pvscan
lvextend -L +130G /dev/rhel/root -r

#Adding -r will grow filesystem after resizing the volume.

Create a UEFI Bootable USB drive (e.g. /dev/sdc1)

sudo dd if=~/path/to/isofile.iso of=/dev/sdc1 oflag=direct bs=1048576

Locate and remove a package

sudo dpkg -l | grep <package_name>
sudo dpkg --purge <package_name>

Create a ssh tunnel

ssh -f -L 9000:targetservername:8088 root@192.168.14.72 -N
#-f: run in background; -L: Listen; -N: do nothing  
#the 9000 of your computer is now connected to the 8088 port of the targetservername through 192.168.14.72  
#so that you can see the content of targetservername:8088 by entering localhost:9000 from your browser.

Get process ID of a process (e.g. sublime_text)

#pidof
pidof sublime_text

#pgrep, you dont have to type the whole program name
pgrep sublim

#top, takes longer time
top|grep sublime_text

Some benchmarking tools for your server

aio-stress - AIO benchmark.
bandwidth - memory bandwidth benchmark.
bonnie++ - hard drive and file system performance benchmark.
dbench - generate I/O workloads to either a filesystem or to a networked CIFS or NFS server.
dnsperf - authorative and recursing DNS servers.
filebench - model based file system workload generator.
fio - I/O benchmark.
fs_mark - synchronous/async file creation benchmark.
httperf - measure web server performance.
interbench - linux interactivity benchmark.
ioblazer - multi-platform storage stack micro-benchmark.
iozone - filesystem benchmark.
iperf3 - measure TCP/UDP/SCTP performance.
kcbench - kernel compile benchmark, compiles a kernel and messures the time it takes.
lmbench - Suite of simple, portable benchmarks.
netperf - measure network performance, test unidirectional throughput, and end-to-end latency.
netpipe - network protocol independent performance evaluator.
nfsometer - NFS performance framework.
nuttcp - measure network performance.
phoronix-test-suite - comprehensive automated testing and benchmarking platform.
seeker - portable disk seek benchmark.
siege - http load tester and benchmark.
sockperf - network benchmarking utility over socket API.
spew - measures I/O performance and/or generates I/O load.
stress - workload generator for POSIX systems.
sysbench - scriptable database and system performance benchmark.
tiobench - threaded IO benchmark.
unixbench - the original BYTE UNIX benchmark suite, provide a basic indicator of the performance of a Unix-like system.
wrk - HTTP benchmark.

Show a listing of last logged in users.

lastb

Show a listing of current logged in users, print information of them

who

Show who is logged on and what they are doing

Print the user names of users currently logged in to the current host.

users

Stop tailing a file on program terminate

tail -f --pid=<PID> filename.txt
# replace <PID> with the process ID of the program.

List all enabled services

systemctl list-unit-files|grep enabled

Hardware

[back to top]

Finding Out memory device detail

sudo dmidecode -t memory

Print detail of CPU hardware

dmidecode -t 4
#          Type   Information
#          0   BIOS
#          1   System
#          2   Base Board
#          3   Chassis
#          4   Processor
#          5   Memory Controller
#          6   Memory Module
#          7   Cache
#          8   Port Connector
#          9   System Slots
#         11   OEM Strings
#         13   BIOS Language
#         15   System Event Log
#         16   Physical Memory Array
#         17   Memory Device
#         18   32-bit Memory Error
#         19   Memory Array Mapped Address
#         20   Memory Device Mapped Address
#         21   Built-in Pointing Device
#         22   Portable Battery
#         23   System Reset
#         24   Hardware Security
#         25   System Power Controls
#         26   Voltage Probe
#         27   Cooling Device
#         28   Temperature Probe
#         29   Electrical Current Probe
#         30   Out-of-band Remote Access
#         31   Boot Integrity Services
#         32   System Boot
#         34   Management Device
#         35   Management Device Component
#         36   Management Device Threshold Data
#         37   Memory Channel
#         38   IPMI Device
#         39   Power Supply

Count the number of Segate hard disks

lsscsi|grep SEAGATE|wc -l
or
sg_map -i -x|grep SEAGATE|wc -l

Get UUID of a disk (e.g. sdb)

blkid /dev/sdb

Print detail of all hard disks

lsblk -io KNAME,TYPE,MODEL,VENDOR,SIZE,ROTA
#where ROTA means rotational device / spinning hard disks (1 if true, 0 if false)

List information about NIC

lspci | egrep -i --color 'network|ethernet'

Found out power status of the server

ipmitool -U your_bmc_username -P your_bmc_userpassword -I lanplus -H your_bmc_ip_address power status

Found out server sensor temperature

ipmitool sensors |grep -i Temp

Others

[back to top]

Remove newline / nextline

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

Replace newline

tr '\n' ' ' <filename

To uppercase/lowercase

tr /a-z/ /A-Z/

Translate a range of characters (e.g. substitute a-z into a)

echo 'something' |tr a-z a
# aaaaaaaaa

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

diff fileA fileB
# a: added; d:delete; c:changed

sdiff fileA fileB
# side-to-side merge of file differences

Compare two files, strip trailing carriage return/ nextline (e.g. fileA, fileB)

 diff fileA fileB --strip-trailing-cr

Number a file (e.g. fileA)

nl fileA

nl -nrz fileA
# add leading zeros

nl -w1 -s ' '
# making it simple, blank seperated

Join two files field by field with tab (default join by the first column of both file, and default separator is space)

# fileA and fileB should have the same ordering of lines.
join -t '\t' fileA fileB
 
# Join using specified field (e.g. column 3 of fileA and column 5 of fileB)
join -1 3 -2 5 fileA fileB

Combine/ paste two or more files into columns (e.g. fileA, fileB, fileC)

paste fileA fileB fileC
# default tab seperated

Reverse string

echo 12345| rev

Read .gz file without extracting

zmore filename

zless filename

Run in background, output error file

some_commands  &>log &

some_commands 2>log &

some_commands 2>&1| tee logfile

some_commands 2>&1 >>outfile
#0: standard input; 1: standard output; 2: standard error

Send mail

echo 'heres the content'| mail -a /path/to/attach_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

history -d [line_number]

Get last history/record filename

head !$

Clean screen

clear

Ctrl+l

Send data to last edited file

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

Extract .xf

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

Install python package

pip install packagename

Delete current bash command

Ctrl+U

Ctrl+C

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

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

Read user input

read input
echo $input

Generate sequence 1-10

seq 10

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 smaller file

# Split by line (e.g. 1000 lines/smallfile)
split -d -l 1000 largefile.txt
 
# Split by byte without breaking lines across files
split -C 10 largefile.txt

Create a large amount of dummy files (e.g 100000 files, 10 bytes each):

#1. Create a big file
dd if=/dev/zero of=bigfile bs=1 count=1000000

#2. Split the big file to 100000 10-bytes files
 split -b 10 -a 10 bigfile

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

rename 's/ABC//' *.gz

Remove file extension (e.g remove .gz from filename.gz)

basename filename.gz .gz

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

Add file extension to all file(e.g add .txt)

rename s/$/.txt/ *
# You can use rename -n s/$/.txt/ * to check the result first, it will only print sth like this:
# rename(a, a.txt)
# rename(b, b.txt)
# rename(c, c.txt)

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/ i++ a numeric variable (e.g. $var)

((var++))
or
var=$((var+1))

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

Unzip tar.xz file (e.g. file.tar.xz)

unxz file.tar.xz
tar xopf file.tar

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
or
dd if=/dev/zero of=//dev/shm/200m bs=1M 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

Press any key to continue

read -rsp $'Press any key to continue...\n' -n1 key

Run sql-like command on files from terminal

download:
https://github.com/harelba/q
example:

q -d "," "select c3,c4,c5 from /path/to/file.txt where c3='foo' and c5='boo'"

Sreen and tmux

create session and attach:

screen
or  
tmux

create detached session foo:

screen -S foo -d -m	
or  
tmux new -s foo -d

detached session foo:

screen: ^a^d
or  
tmux: ^bd

list sessions:

screen -ls	
or  
tmux ls

attach:

screen -r	
or  
tmux attach

attach to session foo:

screen -r foo	
or 
tmux attach -t foo

kill session foo:

screen -r foo -X quit
or  
tmux kill-session -t foo

scroll:
(screeen)
Hit your screen prefix combination (C-a / control+A), then hit Escape.
Move up/down with the arrow keys (↑ and ↓).

Redirect output of an already running process in screen:
(C-a / control+A), then hit 'H'

store screen output for screen:
Ctrl+A, Shift+H
You will then find a screen.log file under current directory.

(tmux)
Ctrl-b then [ then you can use your normal navigation keys to scroll around.
Press q to quit scroll mode.

Send command to all panes in tmux:

Ctrl-B
:setw synchronize-panes

Some tmux pane control commands:

Ctrl-B

#   Panes (splits), Press Ctrl+B, then input the following symbol:
#   %  horizontal split
#   "  vertical split
#   o  swap panes
#   q  show pane numbers
#   x  kill pane
#   space - toggle between layouts

#   Distribute Vertically (rows): 
select-layout even-vertical
#   or
Ctrl+b, Alt+2

#   Distribute horizontally (columns): 
select-layout even-horizontal
#   or
Ctrl+b, Alt+1

Cut the last column

cat filename|rev|cut -f1|rev

pass password to ssh

sshpass -p mypassword ssh root@10.102.14.88 "df -h"

wait for a pid (job) to complete

wait %1 
or 
wait $PID
wait ${!}
#wait ${!} to wait till the last background process ($! is the PID of the last background process)

pdf to txt

sudo apt-get install poppler-utils
pdftotext example.pdf example.txt

list only directory

ls -ld -- */

Capture/record/save terminal output (capture everything you type and output)

script output.txt
#start using terminal 
#to logout the screen session (stop saving the contents), type exit.

list contents of directories in a tree-like format.

tree
#go to the directory you want to list, and type tree (sudo apt-get install tree)
#output:
#one/
#└── two
#    ├── 1
#    ├── 2
#    ├── 3
#    ├── 4
#    └── 5
#

set up virtualenv(sandbox) for python

#1. install virtualenv.
sudo apt-get install virtualenv
#2. Creat a directory (name it .venv or whatever name your want) for your new shiny isolated environment.
virtualenv .venv
#3. source virtual bin
source .venv/bin/activate
#4. you can check check if you are now inside a sandbox.
type pip
#5. Now you can install your pip package, here requirements.txt is simply a txt file containing all the packages you want. (e.g tornado==4.5.3).
pip install -r requirements.txt

Working with json data

#install the useful jq package
#sudo apt-get install jq
#e.g. to get all the values of the 'url' key, simply pipe the json to the following jq command(you can use .[]. to select inner json, i.e jq '.[].url')
jq '.url'

Editing your history

history -w
vi ~/.bash_history
history -r

Decimal to Binary (e.g get binary of 5)

D2B=({0..1}{0..1}{0..1}{0..1}{0..1}{0..1}{0..1}{0..1})
echo -e ${D2B[5]}
#00000101
echo -e ${D2B[255]}
#11111111

Wrap each input line to fit in specified width (e.g 4 integers per line)

echo "00110010101110001101" | fold -w4
#0011
#0010
#1011
#1000
#1101

Sort a file by column and keep the original order

sort -k3,3 -s

Right align a column (right align the 2nd column)

cat file.txt|rev|column -t|rev

To both view and store the output

echo 'hihihihi' | tee outputfile.txt
# use '-a' with tee to append to file.

Show non-printing (Ctrl) characters with cat

cat -v filenme

Convert tab to space

expand filenme

Convert space to tab

unexpand filenme

Display file in octal ( you can also use od to display hexadecimal, decimal, etc)

od filenme

Reverse cat a file

tac filenme

Reverse the result from `uniq -c`

while read a b; do yes $b |head -n $a ;done <test.txt

=-=-=-=-=-::::::::::::::::More coming!!::::::::::::::::-=-=-=-=-=

README.md Unescape Escape

Bash-Oneliner

Handy Bash oneliner commands

Terminal Tricks

Ctrl

Change case

Run history number (e.g. 53)

Run last command

Run last command and change some parameter (e.g. last command: echo 'aaa' -> rerun as: echo 'bbb')

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

Grep

Type of grep

Grep and return only integer

Grep integer with certain number of digits (e.g. 3)

Grep only IP address

Grep whole word (e.g. 'target')

Grep returning lines before and after match (e.g. 'bbo')

Grep string starting with (e.g. 'S')

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

Grep lines without word (e.g. bbo)

Grep lines not begin with string (e.g. #)

Grep variables with space within it (e.g. bbo="some strings")

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

Grep and return number of matching line(e.g. bbo)

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

Case insensitive grep (e.g. bbo/BBO/Bbo)

COLOR the match (e.g. bbo)!

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

Search all files in directory, do not ouput the filenames (e.g. bbo)

Search all files in directory, output ONLY the filenames with matches(e.g. bbo)

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

Grep AND (e.g. A and B)

Regex any singer character (e.g. ACB or AEB)

Regex with or without a certain character (e.g. color or colour)

Grep all content of a fileA from fileB

Grep a tab

Grep variable from variable

Grep strings between a bracket()

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

Skip directory (e.g. bbo)

Sed

Remove the 1st line

Remove the first 100 lines (remove line 1-100)

Remove lines with string (e.g. bbo)

Remove lines whose nth character not equal to a value (e.g. 5th character not equal to 2)

Edit infile (edit and save)

When using variable (e.g. $i), use double quotes " "

Delete/remove empty lines

Delete/remove last line

Delete/remove last character from end of file

Add string to beginning of file (e.g. "[")

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

Add newline to the end

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

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

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

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

Substitution (e.g. replace A by B)

Substitution with wildcard (e.g. replace a line start with aaa= by aaa=/my/new/path)

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

Delete lines with string (e.g. bbo)

Print/get/trim a range of line (e.g. line 500-5000)

Print every nth lines

Print every odd # lines

Print every third line including the first line

Remove leading whitespace and tabs

Remove only leading whitespace

Remove ending commas

Add a column to the end

Add extension of filename to last column

Remove newline\ nextline

Print a particular line (e.g. 123th line)

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

Change delimiter

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

Remove last character of file

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

Awk

Set tab as field separator

Output as tab separated (also as field separator)

README.md