Awesome Open Source
Awesome Open Source


I am glad that you are here! I was working on bioinformatics a few years ago and was amazed by those single-word bash commands which are much faster than my dull scripts, time saved through learning command-line shortcuts and scripting. Recent years I am working on cloud computing and I keep recording those useful commands here. Not all of them is oneliner, but i put effort on making them brief and swift. I am mainly using Ubuntu, Amazon Linux, RedHat, Linux Mint, Mac and CentOS, sorry if the commands don't work on your system.

This blog will focus on simple bash commands for parsing data and Linux system maintenance that i acquired from work and LPIC exam. 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, please correct me anytime, thank you. If you know other cool commands, please teach me!

Here's a more stylish version of Bash-Oneliner~

Handy Bash one-liners

Terminal Tricks

Using Ctrl keys
Ctrl + n : same as Down arrow.
Ctrl + p : same as Up arrow.
Ctrl + r : begins a backward search through command 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 + w : cut the word before the cursor; then Ctrl + y paste it
Ctrl + u : cut the line before the cursor; then Ctrl + y paste it
Ctrl + _ : undo typing.
Ctrl + l : equivalent to clear.
Ctrl + x + Ctrl + e : launch editor defined by $EDITOR to input your command. Useful for multi-line commands.
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 lowercase.
Esc + c
# converts letter under the cursor to uppercase.
Run history number (e.g. 53)
Run last command
# run the previous command using sudo
sudo !!
# of course you need to enter your password
Run last command and change some parameter using caret substitution (e.g. last command: echo 'aaa' -> rerun as: echo 'bbb')
#last command: echo 'aaa'

#echo 'bbb'

#Notice that only the first aaa will be replaced, if you want to replace all 'aaa', use ':&' to repeat it:

Run past command that began with (e.g. cat filename)
# or
# run cat filename again
Bash globbing
# '*' serves as a "wild card" for filename expansion.
/b?n/?at      #/bin/cat

# '?' serves as a single-character "wild card" for filename expansion.
/etc/pa*wd    #/etc/passwd

# ‘[]’ serves to match the character from a range.
ls -l [a-z]*   #list all files with alphabet in its filename.

# ‘{}’ can be used to match filenames with more than one patterns
ls {*.sh,*.py}   #list all .sh and .py files
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.

$DESKTOP_SESSION     current display manager
$EDITOR   preferred text editor.
$LANG   current language.
$PATH   list of directories to search for executable files (i.e. ready-to-run programs)
$PWD    current directory
$SHELL  current shell
$USER   current username
$HOSTNAME   current hostname


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Variable substitution within quotes
# foo=bar
 echo "'$foo'"
# double/single quotes around single quotes make the inner single quotes expand variables
Get the length of variable
var="some string"
echo ${#var}
# 11
Get the first character of the variable
echo "${var:0:1}"

# or
echo ${var%%"${var#?}"}
Remove the first or last string from variable
var="some string"
echo ${var:2}
#me string
Replacement (e.g. remove the first leading 0 )
echo ${var[@]#0}
Replacement (e.g. replace 'a' with ',')
Replace all (e.g. replace all 'a' with ',')
#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 lowercase (Parameter Expansion)
echo ${var,,}
Expand and then execute variable/argument
eval "$cmd"
echo "$bar" # foo


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Arithmetic Expansion in Bash (Operators: +, -, *, /, %, etc)
echo $(( 10 + 5 ))  #15
echo $(( x++ )) #1 , notice that it is still 1, since it's post-incremen
echo $(( x++ )) #2
echo $(( ++x )) #4 , notice that it is not 3 since it's pre-incremen
echo $(( x-- )) #4
echo $(( x-- )) #3
echo $(( --x )) #1
echo $(( x ** y )) #8
Print out the prime factors of a number (e.g. 50)
factor 50
# 50: 2 5 5
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

# Exponent operator
echo "10^2" | bc

# Using variables
echo "var=5;--var"| bc


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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 count number of empty lines
grep -c "^$"
Grep and return only integer
grep -o '[0-9]*'
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 between 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. myvar="some strings")
grep "$myvar" 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
# or
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/*


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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 to file), (e.g. deleting the lines with 'bbo' and save to file)
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 bioinformatics 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
Using environment variable and end-of-line pattern at the same time.
# Use backslash for end-of-line $ pattern, and double quotes for expressing the variable
sed -e "\$s/\$/\n+--$3-----+/"
Delete/remove empty lines
sed '/^\s*$/d'

# or

sed '/^$/d'
Delete/remove last line
sed '$d'
Delete/remove last character from end of file
sed -i '$ s/.$//' filename
Add string to beginning of file (e.g. "[")
sed -i '1s/^/[/' file
Add string at certain line number (e.g. add 'something' to line 1 and line 3)
sed -e '1isomething -e '3isomething'
Add string to end of file (e.g. "]")
sed '$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 separate 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

# To 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/*./}/" $i;done >
Remove newline\ nextline
sed ':a;N;$!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


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Set tab as field separator
awk -F $'\t'
Output as tab separated (also as field separator)
awk -v OFS='\t'
Pass variable
awk -v a="$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 occurrence 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
# For example there are two files:
# 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
# For example there are two files:
# 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)
Give number/index to every row
awk '{printf("%s\t%s\n",NR,$0)}'
Break combine column data into rows
# For example, seperate the following content:
# David    cat,dog
# into
# David    cat
# David    dog

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

# Detail here:
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;}'


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Set tab as delimiter (default:space)
xargs -d\t
Prompt commands before running commands
ls|xargs -L1 -p head
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 files with whitespace in filename (e.g. "hello 2001")
find . -name "*.c" -print0|xargs -0 rm -rf
Show limits on command-line length
xargs --show-limits
# Output from my Ubuntu:
# Your environment variables take up 3653 bytes
# POSIX upper limit on argument length (this system): 2091451
# POSIX smallest allowable upper limit on argument length (all systems): 4096
# Maximum length of command we could actually use: 2087798
# Size of command buffer we are actually using: 131072
# Maximum parallelism (--max-procs must be no greater): 2147483647
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
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
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 '' /etc | xargs sed -i 's/'


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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 there are no subdirectory
replace "www" "w" -- *
# a space before *
Find and output only filename (e.g. "mso")
find mso*/ -name M* -printf "%f\n"
Find large files in the system (e.g. >4G)
find / -type f -size +4G
Find and delete file with size less than (e.g. 74 byte)
find . -name "*.mso" -size -74c -delete

# M for MB, etc
Find empty (0 byte) files
find . -type f -empty
# to further delete all the empty files
find . -type f -empty -delete
Recursively count all the files in a directory
find . -type f | wc -l

Condition and loop

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If statement
# 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 echo -e "file contains the string!" ; fi

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

# if variable is null
if [ ! -s "myvariable" ]; then echo -e "variable is null!" ; fi
#True of the length if "STRING" is zero.

# Using test command (same as []), to test if the length of variable is nonzero
test -n "$myvariable" && echo myvariable is "$myvariable" || echo myvariable is not set

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

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

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

# Test if the value of x is greater or equal than 5, in bash/ksh/zsh:
if ((x >= 5)); then echo -e "greater or equal than 5!" ; fi

# Use (( )) for arithmetic operation
if ((j==u+2)); then echo -e "j==u+2!!" ; fi

# Use [[ ]] for comparison
if [[ $age -gt 21 ]]; then echo -e "forever 21!!" ; fi

More if commands

For loop
# Echo the file name under the current directory
for i in $(ls); do echo file $i;done
for i in *; do echo file $i; done

# Make directories listed in a file (e.g. myfile)
for dir in $(<myfile); do mkdir $dir; 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,
oifs="$IFS"; IFS=$'\n'; for line in $(cat myfile); do ...; done
while read -r line; do ...; done <myfile

#If only one word a line, simply
for line in $(cat myfile); do echo $line; read -n1; done

#Loop through an array
for i in "${arrayName[@]}"; do echo $i;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) immediately after it. (BETTER use the wait command! Ctrl+F 'wait')
while [[ $(pidof perl) ]];do echo f;sleep 10;done && python
switch (case in bash)
read type;
case $type in
    echo 'how'
    echo 'are'
    echo 'you'


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Find out the time require for executing a command
time echo hi
Wait for some time (e.g 10s)
sleep 10
Print date with formatting
date +%F
# 2020-07-19

# or
date +'%d-%b-%Y-%H:%M:%S'
# 10-Apr-2020-21:54:40

# Returns the current time with nanoseconds.
date +"%T.%N"
# 11:42:18.664217000  

# Get the seconds since epoch (Jan 1 1970) for a given date (e.g Mar 16 2021)
date -d "Mar 16 2021" +%s
# 1615852800
# or
date -d "Tue Mar 16 00:00:00 UTC 2021"  +%s
# 1615852800  

# Convert the number of seconds since epoch back to date
date --date @1615852800
# Tue Mar 16 00:00:00 UTC 2021

wait for random duration (e.g. sleep 1-5 second, like adding a jitter)
sleep $[ ( $RANDOM % 5 ) + 1 ]
Log out your account after a certain period of time (e.g 10 seconds)
#once you set this variable, logout timer start running!
Set how long you want to run a command
#This will run the command '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


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Download the content of this (the one your are viewing now)
curl | pandoc -f markdown -t man | man -l -

# or w3m (a text based web browser and pager)
curl | pandoc | w3m -T text/html

# or using emacs (in emac text editor)
emacs --eval '(org-mode)' --insert <(curl | pandoc -t org)

# or using emacs (on terminal, exit using Ctrl + x then Ctrl + c)
emacs -nw --eval '(org-mode)' --insert <(curl | pandoc -t org)
Download all from a page
wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off

# -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 (separate by ,)
# -e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry
Upload a file to web and download (
#  Upload a file (e.g. filename.txt):
curl --upload-file ./filename.txt
# the above command will return a URL, e.g:

# Next you can download it by:
curl -o filename.txt
Download file if necessary
if [ ! -s $data ];then
    echo "downloading test data..."
    wget $url
Wget to a filename (when a long name)
wget -O filename ""
Wget files to a folder
wget -P /path/to/directory ""
Instruct curl to follow any redirect until it reaches the final destination:
curl -L


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Random generate password (e.g. generate 5 password each of length 13)
sudo apt install pwgen
pwgen 13 5
#sahcahS9dah4a xieXaiJaey7xa UuMeo0ma7eic9 Ahpah9see3zai acerae7Huigh7
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))


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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 [email protected]_address

# or setting through xhost
# --> Install the following for Centos:
# xorg-x11-xauth
# xorg-x11-fonts-*
# xorg-x11-utils
Little xwindow tools
Open pictures/images from ssh server
1. ssh -X [email protected]_address
2. apt-get install eog
3. eog picture.png
Watch videos on server
1. ssh -X [email protected]_address
2. sudo apt install mpv
3. mpv myvideo.mp4
Use gedit on server (GUI editor)
1. ssh -X [email protected]_address
2. apt-get install gedit
3. gedit filename.txt
Open PDF file from ssh server
1. ssh -X [email protected]_address
2. apt-get install evince
3. evince filename.pdf
Use google-chrome browser from ssh server
1. ssh -X [email protected]_address
2. apt-get install libxss1 libappindicator1 libindicator7
3. wget
4. sudo apt-get install -f
5. dpkg -i google-chrome*.deb
6. google-chrome


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Work with yum history
# List yum history (e.g install, update)
sudo yum history
# Example output:
# Loaded plugins: extras_suggestions, langpacks, priorities, update-motd
# ID     | Login user               | Date and time    | Action(s)      | Altered
# -------------------------------------------------------------------------------
#     11 |  ... <myuser>       | 2020-04-10 10:57 | Install        |    1 P<
#     10 |  ... <myuser>       | 2020-03-27 05:21 | Install        |    1 >P
#      9 |  ... <myuser>       | 2020-03-05 11:57 | I, U           |   56 *<
# ...

# Show more details of a yum history (e.g. history #11)
sudo yum history info 11

# Undo a yum history (e.g. history #11, this will uninstall some packages)
sudo yum history undo 11
Audit files to see who made changes to a file [RedHat based system only]
# To audit a directory recursively for changes (e.g. myproject)
auditctl -w /path/to/myproject/ -p wa

# If you delete a file name "VIPfile", the deletion is recorded in /var/log/audit/audit.log
sudo grep VIPfile /var/log/audit/audit.log
#type=PATH msg=audit(1581417313.678:113): item=1 name="VIPfile" inode=300115 dev=ca:01 mode=0100664 ouid=1000 ogid=1000 rdev=00:00 nametype=DELETE cap_fp=0000000000000000 cap_fi=0000000000000000 cap_fe=0 cap_fver=0
Check out whether SELinux is enabled
# SELinux status:                 enabled
# SELinuxfs mount:                /sys/fs/selinux
# SELinux root directory:         /etc/selinux
# Loaded policy name:             targeted
# Current mode:                   enforcing
# Mode from config file:          enforcing
# Policy MLS status:              enabled
# Policy deny_unknown status:     allowed
# Max kernel policy version:      31
Generate public key from private key
ssh-keygen -y -f ~/.ssh/id_rsa > ~/.ssh/
Copy your default public key to remote user
ssh-copy-id <user_name>@<server_IP>
# then you need to enter the password
# and next time you won't need to enter password when ssh to that user
Copy default public key to remote user using the required private key (e.g. use your mykey.pem key to copy your to the remote user)
# before you need to use mykey.pem to ssh to remote user.
ssh-copy-id -i ~/.ssh/ -o "IdentityFile ~/Downloads/mykey.pem" <user_name>@<server_IP>
# now you don't need to use key to ssh to that user.
SSH Agent Forwarding
# To bring your key with you when ssh to serverA, then ssh to serverB from serverA using the key.
ssh-add /path/to/mykey.pem
ssh -A <username>@<IP_of_serverA>
# Next you can ssh to serverB
ssh <username>@<IP_of_serverB>
Set the default user and key for a host when using SSH
# add the following to ~/.ssh/config
Host myserver
  User myuser
  IdentityFile ~/path/to/mykey.pem

# Next, you could run "ssh myserver" instead of "ssh -i ~/path/to/mykey.pem [email protected]"
Follow the most recent logs from service
journalctl -u <service_name> -f
Eliminate the zombie
# A zombie is already dead, so you cannot kill it. You can eliminate the zombie by killing its parent.
# First, find PID of the zombie
ps aux| grep 'Z'
# Next find the PID of zombie's parent
pstree -p -s <zombie_PID>
# Then you can kill its parent and you will notice the zombie is gone.
sudo kill 9 <parent_PID>
Show memory usage
free -c 10 -mhs 1
# print 10 times, at 1 second interval
Display CPU and IO statistics for devices and partitions.
# refresh every second
iostat -x -t 1
Display bandwidth usage on an network interface (e.g. enp175s0f0)
iftop -i enp175s0f0
Tell how long the system has been running and number of users
Check if it's root running
if [ "$EUID" -ne 0 ]; then
        echo "Please run this as root"
        exit 1
Change shell of a user (e.g. bonnie)
chsh -s /bin/sh bonnie
# /etc/shells: valid login shells
Change root / fake root / jail (e.g. change root to newroot)
chroot /home/newroot /bin/bash

# To exit chroot
Display file status (size; access, modify and change time, etc) of a file (e.g. filename.txt)
stat filename.txt
Snapshot of the current processes
ps aux
Display a tree of processes
Find maximum number of processes
cat /proc/sys/kernel/pid_max
Print or control the kernel ring buffer
Show IP address
$ip add show

# or
Print previous and current SysV runlevel

# or
who -r
Change SysV runlevel (e.g. 5)
init 5
telinit 5
Display all available services in all runlevels,
chkconfig --list
# update-rc.d equivalent to chkconfig in ubuntu
Check system version
cat /etc/*-release
Linux Programmer's Manuel: hier- description of the filesystem hierarchy
man hier
Control the systemd system and service manager
# e.g. check the status of cron service
systemctl status cron.service

# e.g. stop cron service
systemctl stop cron.service
List job
jobs -l
Run a program with modified priority (e.g. ./
# nice value is adjustable from -20 (most favorable) to +19
# the nicer the application, the lower the priority
# Default niceness: 10; default priority: 80

nice -10 ./
Export PATH
export PATH=$PATH:~/path/you/want
Make file executable
chmod +x filename
# you can now ./filename to execute it
Print system information
uname -a

# Check system hardware-platform (x86-64)
uname -i
Surf the net
Add user, set passwd
useradd username
passwd username
Edit PS1 variable for bash (e.g. displaying the whole path)
1. vi ~/.bash_profile
2. export PS1='\[email protected]\h:\w\$'
# $PS1 is a variable that defines the makeup and style of the command prompt
# You could use emojis and add timestamp to every prompt using the following value:
# export PS1="\[email protected]🦁:\w\$ "
3. source ~/.bash_profile
Edit environment setting (e.g. alias)
1. vi ~/.bash_profile
2. alias pd="pwd" //no more need to type that 'w'!
3. source ~/.bash_profile
Print all alias
alias -p
Unalias (e.g. after alias ls='ls --color=auto')
unalias ls
Set and unset shell options
# print all shell options

# to unset (or stop) alias
shopt -u expand_aliases

# to set (or start) alias
shopt -s expand_aliases
List environment variables (e.g. PATH)
echo $PATH
# list of directories separated by a colon
List all environment variables for current user
Unset environment variable (e.g. unset variable 'MYVAR')
unset MYVAR
Show partition format
Inform the OS of partition table changes
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
Print resolved symbolic links or canonical file names
readlink filename
Find out the type of command and where it link to (e.g. python)
type python
# python is /usr/bin/python
# There are 5 different types, check using the 'type -f' flag
# 1. alias    (shell alias)
# 2. function (shell function, type will also print the function body)
# 3. builtin  (shell builtin)
# 4. file     (disk file)
# 5. keyword  (shell reserved word)

# You can also use `which`
which python
# /usr/bin/python
List all functions names
declare -F
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 .

# then pop

#or use dirs to display the list of currently remembered directories.
dirs -l
Show disk usage
df -h

# or
du -h

du -sk /var/log/* |sort -rn |head -10
check the Inode utilization
df -i
# Filesystem      Inodes  IUsed   IFree IUse% Mounted on
# devtmpfs        492652    304  492348    1% /dev
# tmpfs           497233      2  497231    1% /dev/shm
# tmpfs           497233    439  496794    1% /run
# tmpfs           497233     16  497217    1% /sys/fs/cgroup
# /dev/nvme0n1p1 5037976 370882 4667094    8% /
# tmpfs           497233      1  497232    1% /run/user/1000
Show all file system type
df -TH
Show current runlevel
Switch runlevel
init 3

telinit 3
Permanently modify runlevel
1. edit /etc/init/rc-sysinit.conf
Become root
Become somebody
su somebody
Report user quotes on device
repquota -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
Mount and unmount
# e.g. Mount /dev/sdb to /home/test
mount /dev/sdb /home/test

# e.g. Unmount /home/test
umount /home/test
List current mount detail
# or
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

# variable for UID
echo $UID
Check if it's root
if [ $(id -u) -ne 0 ];then
    echo "You are not root!"
# 'id -u' output 0 if it's not root
Find out CPU information
more /proc/cpuinfo

# or
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
Display current libraries from the cache
ldconfig -p
Print shared library dependencies (e.g. for 'ls')
ldd /bin/ls
Check user login
Check last reboot history
last reboot
Edit path for all users
joe /etc/environment
# edit this file
Show and set user limit
ulimit -u
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
Broadcast 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;
# or
yum install dconf dconf-editor;
yum install dbus dbus-x11;

# Check list
gsettings list-recursively

# Change some settings
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 check with:
# Or check /etc/hostname

# If still not working..., edit:
#add HOSTNAME="your-new-hostname"
List installed packages
apt list --installed

# or on Red Hat:
yum list installed
Check for package update
apt list --upgradeable

# or
sudo yum check-update
Run yum update excluding a package (e.g. do not update php packages)
sudo yum update --exclude=php*
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
Tutorial for setting up your own DNS server

Tutorial for creating a simple daemon

Tutorial for using your gmail to send email

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

# or
ps aux|grep python
Check status of a process using PID
ps -p <PID>

cat /proc/<PID>/status
cat /proc/<PID>/stack
cat /proc/<PID>/stat
# Start ntp:

# 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)
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 [email protected] -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
#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 sublime_text

#pgrep, you don't have to type the whole program name
pgrep sublim

#pgrep, echo 1 if process found, echo 0 if no such process
pgrep -q sublime_text && echo 1 || echo 0

#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 measures 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.

Performance monitoring tool - sar
# installation
# It collects the data every 10 minutes and generate its report daily. crontab file (/etc/cron.d/sysstat) is responsible for collecting and generating reports.
yum install sysstat
systemctl start sysstat
systemctl enable sysstat

# show CPU utilization 5 times every 2 seconds.
sar 2 5

# show memory  utilization 5 times every 2 seconds.
sar -r 2 5

# show paging statistics 5 times every 2 seconds.
sar -B 2 5

# To generate all network statistic:
sar -n ALL

# reading SAR log file using -f
sar -f /var/log/sa/sa31|tail
Reading from journal file
journalctl --file ./log/journal/a90c18f62af546ccba02fa3734f00a04/system.journal  --since "2020-02-11 00:00:00"
Show a listing of last logged in users.
Show a listing of current logged in users, print information of them
Show who is logged on and what they are doing
Print the user names of users currently logged in to the current host.
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


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Collect and summarize all hardware info of your machine
lshw -json >report.json
# Other options are: [ -html ]  [ -short ]  [ -xml ]  [ -json ]  [ -businfo ]  [ -sanitize ] ,etc
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)
lsblk -f /dev/sdb

# or
sudo blkid /dev/sdb
Generate an UUID
Print detail of all hard disks
#where ROTA means rotational device / spinning hard disks (1 if true, 0 if false)
List all PCI (Peripheral Component Interconnect) devices
# List information about NIC
lspci | egrep -i --color 'network|ethernet'
List all USB devices
Linux modules
# Show the status of modules in the Linux Kernel

# Add and remove modules from the Linux Kernel

# or
# Remove a module

# Insert a module
Controlling IPMI-enabled devices (e.g. BMC)
# Remotely finding out power status of the server
ipmitool -U <bmc_username> -P <bmc_password> -I lanplus -H <bmc_ip_address> power status

# Remotely switching on server
ipmitool -U <bmc_username> -P <bmc_password> -I lanplus -H <bmc_ip_address> power on

# Turn on panel identify light (default 15s)
ipmitool chassis identify 255

# Found out server sensor temperature
ipmitool sensors |grep -i Temp

# Reset BMC
ipmitool bmc reset cold

# Prnt BMC network
ipmitool lan print 1

# Setting BMC network
ipmitool -I bmc lan set 1 ipaddr
ipmitool -I bmc lan set 1 netmask
ipmitool -I bmc lan set 1 defgw ipaddr


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Resolve a domain to IP address(es)
dig +short

# or
Get DNS TXT record a of domain
dig -t txt

# or
host -t txt
Send a ping with a limited TTL to 10 (TTL: Time-To-Live, which is the maximum number of hops that a packet can travel across the Internet before it gets discarded.)
ping -t 10
Print the route packets trace to network host
Check connection to host (e.g. check connection to port 80 and 22 of
nc -vw5 80
# Connection to 80 port [tcp/http] succeeded!

nc -vw5 22
# nc: connect to port 22 (tcp) timed out: Operation now in progress
# nc: connect to port 22 (tcp) failed: Network is unreachable
Nc as a chat tool!
# From server A:
$ sudo nc -l 80
# then you can connect to the 80 port from another server (e.g. server B):
# e.g. telent <server A IP address> 80
# then type something in server B
# and you will see the result in server A!
Check which ports are listening for TCP connections from the network
#notice that some companies might not like you using nmap
nmap -sT -O localhost

# check port 0-65535
nmap  -p0-65535 localhost
Check if a host is up and scan for open ports, also skip host discovery.
#skips checking if the host is alive which may sometimes cause a false positive and stop the scan.
$ nmap -Pn

# Example output:
# Starting Nmap 7.01 ( ) at 2020-07-18 22:59 CST
# Nmap scan report for (
# Host is up (0.013s latency).
# Other addresses for (not scanned): 2404:6800:4008:802::200e
# rDNS record for
# Not shown: 998 filtered ports
# 80/tcp  open  http
# 443/tcp open  https
# Nmap done: 1 IP address (1 host up) scanned in 3.99 seconds
Scan for open ports and OS and version detection (e.g. scan the domain "")
$ nmap -A -T4
# -A to enable OS and version detection, script scanning, and traceroute; -T4 for faster execution
Look up website information (e.g. name server), searches for an object in a RFC 3912 database.
Show the SSL certificate of a domain
openssl s_client -showcerts -connect
Display IP address
ip a
Display route table
ip r
Display ARP cache (ARP cache displays the MAC addresses of device in the same network that you have connected to)
ip n
Add transient IP addres (reset after reboot) (e.g. add to device eno16777736)
ip address add dev eno16777736
Persisting network configuration changes
sudo vi /etc/sysconfig/network-scripts/ifcfg-enoxxx
# then edit the fields: BOOTPROT, DEVICE, IPADDR, NETMASK, GATEWAY, DNS1 etc
Refresh NetworkManager
sudo nmcli c reload
Restart all interfaces
sudo systemctl restart network.service
To view hostname, OS, kernal, architecture at the same time!
Set hostname (set all transient, static, pretty hostname at once)
hostnamectl set-hostname "mynode"
Find out the web server (e.g Nginx or Apache) of a website
curl -I
# HTTP/1.1 200 OK
# Server: nginx
# Date: Thu, 02 Jan 2020 07:01:07 GMT
# Content-Type: text/html
# Content-Length: 1119
# Connection: keep-alive
# Vary: Accept-Encoding
# Last-Modified: Mon, 09 Sep 2019 10:37:49 GMT
# ETag: "xxxxxx"
# Accept-Ranges: bytes
# Vary: Accept-Encoding
Find out the http status code of a URL
curl -s -o /dev/null -w "%{http_code}"
Unshorten a shortended URL
curl -s -o /dev/null -w "%{redirect_url}"
Perform network throughput tests
# server side:
$ sudo iperf -s -p 80

# client side:
iperf -c <server IP address> --parallel 2 -i 1 -t 2 -p 80
To block port 80 (HTTP server) using iptables.
sudo iptables -A INPUT -p tcp --dport 80 -j DROP

# only block connection from an IP address
sudo iptables –A INPUT –s <IP> -p tcp –dport 80 –j DROP

Data wrangling

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Print some words that start with a particular string (e.g. words start with 'phy')
# If file is not specified, the file /usr/share/dict/words is used.
look phy|head -n 10
# Phil
# Philadelphia
# Philadelphia's
# Philby
# Philby's
# Philip
# Philippe
# Philippe's
# Philippians
# Philippine
Repeat printing string n times (e.g. print 'hello world' five times)
printf 'hello world\n%.0s' {1..5}
Do not echo the trailing newline
username=`echo -n "bashoneliner"`
Copy a file to multiple files (e.g copy fileA to file(B-D))
tee <fileA fileB fileC fileD >/dev/null
Delete all non-printing characters
tr -dc '[:print:]' < filename
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

# or
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 separate
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 separate
Group/combine rows into one row
# e.g.
cat filename|paste - -
cat filename|paste - - - -
Fastq to fasta (fastq and fasta are common file formats for bioinformatics sequence data)
cat file.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' >file.fa
Reverse string
echo 12345| rev
Generate sequence 1-10
seq 10
Find average of input list/file of integers
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
    bash -c "echo "$repetition""
Read file content to variable
Echo size of variable
echo ${#foo}
Echo a tab
echo -e ' \t '
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)
Squeeze repeat patterns (e.g. /t/t --> /t)
tr -s "/t" < filename
Do not print nextline with echo
echo -e 'text here \c'
View first 50 characters of file
head -c 50 file
Cut and get last column of a file
cat file|rev | cut -d/ -f1 | rev
Add one to variable/increment/ i++ a numeric variable (e.g. $var)
# or

Cut the last column
cat filename|rev|cut -f1|rev
Cat to a file
cat >myfile
let me add sth here
exit by control + c
Clear the contents of a file (e.g. filename)
Append to file (e.g. hihi)
echo 'hihi' >>filename
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')
cat file.json | jq '.url'
Decimal to Binary (e.g get binary of 5)
echo -e ${D2B[5]}
echo -e ${D2B[255]}
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 filename
Convert tab to space
expand filename
Convert space to tab
unexpand filename
Display file in octal ( you can also use od to display hexadecimal, decimal, etc)
od filename
Reverse cat a file
tac filename
Reverse the result from uniq -c
while read a b; do yes $b |head -n $a ;done <test.txt


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Describe the format and characteristics of image files.
identify myimage.png
#myimage.png PNG 1049x747 1049x747+0+0 8-bit sRGB 1.006MB 0.000u 0:00.000
Bash auto-complete (e.g. show options "now tomorrow never" when you press'tab' after typing "dothis")

More examples

complete -W "now tomorrow never" dothis
# ~$ dothis  
# never     now       tomorrow
# press 'tab' again to auto-complete after typing 'n' or 't'
Displays a calendar
# print the current month, today will be highlighted.
# October 2019      
# Su Mo Tu We Th Fr Sa  
#    1  2  3  4  5  
# 6  7  8  9 10 11 12  
# 13 14 15 16 17 18 19  
# 20 21 22 23 24 25 26  
# 27 28 29 30 31  

# only display November
cal -m 11
Convert the hexadecimal MD5 checksum value into its base64-encoded format.
openssl md5 -binary /path/to/file| base64
# NWbeOpeQbtuY0ATWuUeumw==
Forces applications to use the default language for output
export LC_ALL=C

# to revert:
unset LC_ALL
Encode strings as Base64 strings
echo test|base64
Get parent directory of current directory
dirname `pwd`
Read .gz file without extracting
zmore filename

# or
zless filename
Run command in background, output error file
some_commands  &>log &

# or
some_commands 2>log &

# or
some_commands 2>&1| tee logfile

# or
some_commands |& tee logfile

# or
some_commands 2>&1 >>outfile
#0: standard input; 1: standard output; 2: standard error
Run multiple commands in background
# run sequentially
(sleep 2; sleep 3) &

# run parallelly
sleep 2 & sleep 3 &
Run process even when logout (immune to hangups, with output to a non-tty)
# e.g. Run even when log out.
nohup bash
Send mail
echo 'heres the content'| mail -a /path/to/attach_file.txt -s 'mail.subject' [email protected]
# use -a flag to set send from (-a "From: [email protected]")
Convert .xls to csv
xls2csv 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
Editing your history
history -w
vi ~/.bash_history
history -r

history -d [line_number]
Interacting with history
# list 5 previous command (similar to `history |tail -n 5` but wont print the history command itself)
fc -l -5
Delete current bash command

# or

# or
# to make it to history
Add something to history (e.g. "addmetohistory")
# addmetodistory
# just add a "#" before~~
Get last history/record filename
head !$
Clean screen
# or simply Ctrl+l
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 [email protected]_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
Use backslash "" to break long command
cd tmp/a/b/c \
> || \
>mkdir -p tmp/a/b/c
List file type of file (e.g. /tmp/)
file /tmp/
# tmp/: directory
Writing Bash script ('#!'' is called shebang )
# remove string before a "."
Python simple HTTP Server
python -m SimpleHTTPServer
# or when using python3:
python3 -m http.server
Read user input
read input
echo $input
declare -a array=()

# or
declare array=()

# or associative array
declare -A array=()
Send a directory
scp -r directoryname [email protected]:/path/to/send
Fork bomb
# Don't try this at home!
# It is a function that calls itself twice every call until you run out of system resources.
# A '# ' is added in front for safety reason, remove it when seriously you are testing it.
# :(){:|:&};:
Use the last argument
Check last exit code
echo $?
Extract .xz
unxz filename.tar.xz
# then
tar -xf filename.tar
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
Extract to a path
tar xvf -C /path/to/directory filename.gz
Zip the content of a directory without including the directory itself
# First cd to the directory, they run:
zip -r -D ../myzipfile .
# you will see the in the parent directory (cd ..)
Output a y/n repeatedly until killed
# 'y':

# or 'n':
yes n

# or 'anything':
yes anything

# pipe yes to other command
yes | rm -r large_directory
Create large dummy file of certain size instantly (e.g. 10GiB)
fallocate -l 10G 10Gigfile
Create dummy file of certain size (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
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)
Colorful (and useful) version of top (install htop first)
Press any key to continue
read -rsp $'Press any key to continue...\n' -n1 key
Run sql-like command on files from terminal
# download:
# example:
q -d "," "select c3,c4,c5 from /path/to/file.txt where c3='foo' and c5='boo'"
Using Screen for multiple terminal sessions
# Create session and attach:

# Create a screen and name it 'test'
screen -S test

# Create detached session foo:
screen -S foo -d -m

# Detached session foo:
screen: ^a^d

# List sessions:
screen -ls

# Attach last session:
screen -r

# Attach to session foo:
screen -r foo

# Kill session foo:
screen -r foo -X quit

# Scroll:
# 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.  
Using Tmux for multiple terminal sessions
# Create session and attach:

# Attach to session foo:
tmux attach -t foo

# Detached session foo:

# List sessions:
tmux ls

# Attach last session:
tmux attach

# Kill session foo:
tmux kill-session -t foo

# Create detached session foo:
tmux new -s foo -d

# Send command to all panes in tmux:
:setw synchronize-panes

# Some tmux pane control commands:
#   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

# Scroll
Ctrl-b then \[ then you can use your normal navigation keys to scroll around.
Press q to quit scroll mode.
Pass password to ssh
sshpass -p mypassword ssh [email protected] "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)
Convert pdf to txt
sudo apt-get install poppler-utils
pdftotext example.pdf example.txt
List only directory
ls -d */
List one file per line.
ls -1
# or list all, do not ignore entries starting with .
ls -1a
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.
# go to the directory you want to list, and type tree (sudo apt-get install tree)
# output:
# home/
# └── project
#     ├── 1
#     ├── 2
#     ├── 3
#     ├── 4
#     └── 5

# set level directories deep (e.g. level 1)
tree -L 1
# home/
# └── project
Set up virtualenv(sandbox) for python
# 1. install virtualenv.
sudo apt-get install virtualenv
# 2. Create 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
# 6. Exit virtual environment

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