# Bash-Oneliner Hi bash learners and bioinformaticans, welcome to Bash Oneliner. I started studying bioinformatics data three years ago, and was amazed by those single-word bash commands which are much faster than my dull scripts, so i started bash. Not all the code here is oneliner (if the ';' counts..), but i put effort on making them brief and fast. This blog will focus on simple bash commands for parsing biological data, most of which are for tsv files (tab-separated values); some of them are for Ubuntu system maintaining. I have been recording the bash commands on my notebook, but putting them on web will help others and myself to query. I apologize that there won't be any citation for the codes, but they are probably from dear Google and Stackoverflow. English and bash are not my first language, so... correct me anytime, thank you In case you would like to check and vote up my questions on Stackoverflow, here's my page: http://stackoverflow.com/users/4290753/once Here's a more stylish version~ http://onceupon.github.io/Bash-Oneliner/ ## Handy Bash oneliner commands for tsv file editing - [Grep](#grep) - [Sed](#sed) - [Awk](#awk) - [Xargs](#xargs) - [Find](#find) - [Loops](#loops) - [Download](#download) - [Random](#random) - [Xwindow](#xwindow) - [Others](#others) - [System](#system) ## Grep ##### Extract text bewteen words (e.g. w1,w2) ```bash grep -o -P '(?<=w1).*(?=w2)' ``` ##### Grep lines without word (e.g. bbo) ```bash grep -v bbo filename ``` ##### Grep only one/first match (e.g. bbo) ```bash grep -m 1 bbo filename ``` ##### Grep and count (e.g. bbo) ```bash grep -c bbo filename ``` ##### Insensitive grep (e.g. bbo/BBO/Bbo) ```bash grep -i "bbo" filename ``` ##### Count occurrence (e.g. three times a line count three times) ```bash grep -o bbo filename ``` ##### COLOR the match (e.g. bbo)! ```bash grep --color bbo filename ``` ##### Grep search all files in a directory(e.g. bbo) ```bash grep -R bbo /path/to/directory ``` or ```bash grep -r bbo /path/to/directory ``` ##### Search all files in directory, only output file names with matches(e.g. bbo) ```bash grep -Rh bbo /path/to/directory ``` or ```bash grep -rh bbo /path/to/directory ``` ##### Grep OR (e.g. A or B or C or D) ``` grep 'A\|B\|C\|D' ``` ##### Grep AND (e.g. A and B) ```bash grep 'A.*B' ``` ##### Grep all content of a fileA from fileB ```bash grep -f fileA fileB ``` ##### Grep a tab ```bash grep $'\t' ``` ##### Grep variable from variable ```bash $echo "$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() ```bash grep -oP '\(\K[^\)]+' ``` ##### Grep number of characters with known strings in between(e.g. AAEL000001-RA) ```bash grep -o -w "\w\{10\}\-R\w\{1\}" ``` // \w word character [0-9a-zA-Z_] \W not word character ##### A lot examples here http://www.cyberciti.biz/faq/grep-regular-expressions/ ## Sed [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Remove lines with word (e.g. bbo) ```bash sed "/bbo/d" filename ``` ##### Edit infile (edit and save) ```bash 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) ```bash sed "1i >$i" ``` //notice the double quotes! in other examples, you can use a single quote, but here, no way! //'1i' means insert to first line ##### Delete empty lines ```bash sed '/^\s*$/d' ``` or ```bash sed 's/^$/d' ``` ##### Delete last line ```bash sed '$d' ``` ##### Delete last character from end of file ```bash sed -i '$ s/.$//' filename ``` ##### Add string to end of file (e.g. "]") ```bash sed '$s/$/]/' filename ``` ##### Add newline to the end ```bash sed '$a\' ``` ##### Add string to beginning of every line (e.g. bbo) ```bash sed -e 's/^/bbo/' file ``` ##### Add string to end of each line (e.g. "}") ```bash sed -e 's/$/\}\]/' filename ``` ##### Add \n every nth character (e.g. every 4th character) ```bash sed 's/.\{4\}/&\n/g' ``` ##### Concatenate/combine/join files with a seperator and next line (e.g seperate by ",") ```bash sed -s '$a,' *.json > all.json ``` ##### Substitution (e.g. replace A by B) ```bash sed 's/A/B/g' filename ``` ##### Select lines start with string (e.g. bbo) ```bash sed -n '/^@S/p' ``` ##### Delete lines with string (e.g. bbo) ```bash sed '/bbo/d' filename ``` ##### Print every nth lines ```bash sed -n '0~3p' filename ``` //catch 0: start; 3: step ##### Print every odd # lines ```bash sed -n '1~2p' ``` ##### Print every third line including the first line ```bash sed -n '1p;0~3p' ``` ##### Remove leading whitespace and tabs ```bash sed -e 's/^[ \t]*//' ``` //notice a whitespace before '\t'!! ##### Remove only leading whitespace ```bash sed 's/ *//' ``` //notice a whitespace before '*'!! ##### Remove ending commas ```bash sed 's/,$//g' ``` ##### Add a column to the end ```bash sed "s/$/\t$i/" ``` //$i is the valuable you want to add e.g. add the filename to every last column of the file ```bash for i in $(ls);do sed -i "s/$/\t$i/" $i;done ``` ##### Add extension of filename to last column ```bash for i in T000086_1.02.n T000086_1.02.p;do sed "s/$/\t${i/*./}/" $i;done >T000086_1.02.np ``` ##### Remove newline\ nextline ```bash sed ':a;N;$!ba;s/\n//g' ``` ##### Print a number of lines (e.g. line 10th to line 33 rd) ```bash sed -n '10,33p' AAA#AAA) ```bash`` sed -r -e 's/^.{3}/&#/' file ``` ## Awk [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Set tab as field separator ```bash awk -F $'\t' ``` ##### Output as tab separated (also as field separator) ```bash awk -v OFS='\t' ``` ##### Pass variable ```bash a=bbo;b=obb; awk -v a="$a" -v b="$b" "$1==a && $10=b' filename ``` ##### Print line number and number of characters on each line ```bash awk '{print NR,length($0);}' filename ``` ##### Find number of columns ```bash awk '{print NF}' ``` ##### Reverse column order ```bash awk '{print $2, $1}' ``` ##### Check if there is a comma in a column (e.g. column $1) ```bash awk '$1~/,/ {print}' ``` ##### Split and do for loop ```bash 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) ```bash awk -v N=7 '{print}/bbo/&& --N<=0 {exit}' ``` ##### Print filename and last line of all files in directory ```bash 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) ```bash awk 'BEGIN{OFS="\t"}$3="chr"$3' ``` ##### Remove lines with string (e.g. bbo) ```bash awk '!/bbo/' file ``` ##### Column subtraction ```bash cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}' ``` ##### Usage and meaning of NR and FNR e.g. fileA: a b c fileB: d e ```bash 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 ```bash 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) ```bash 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 ```bash 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 ```bash awk '{split($2,a,",");for(i in a)print $1"\t"a[i]}' file ``` ##### Sum up a file (each line in file contains only one number) ```bash awk '{s+=$1} END {print s}' filename ``` ##### Average a file (each line in file contains only one number) ```bash awk '{s+=$1}END{print s/NR}' ``` ##### Print field start with string (e.g Linux) ```bash awk '$1 ~ /^Linux/' ``` ##### Sort a row (e.g. 1 40 35 12 23 --> 1 12 23 35 40) ```bash 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) ```bash awk '{$6 = $4 - prev5; prev5 = $5; print;}' ``` ## Xargs [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Set tab as delimiter (default:space) ```bash xargs -d\t ``` ##### Display 3 items per line ```bash echo 1 2 3 4 5 6| xargs -n 3 ``` //1 2 3 4 5 6 ##### Prompt before execution ```bash echo a b c |xargs -p -n 3 ``` ##### Print command along with output ```bash xargs -t abcd ``` ///bin/echo abcd //abcd ##### With find and rm ```bash find . -name "*.html"|xargs rm -rf ``` ##### Delete fiels with whitespace in filename (e.g. "hello 2001") ```bash find . -name "*.c" -print0|xargs -0 rm -rf ``` ##### Show limits ```bash xargs --show-limits ``` ##### Move files to folder ```bash find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old ``` or ```bash find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old ``` ##### Move first 100th files to a directory (e.g. d1) ```bash ls |head -100|xargs -I {} mv {} d1 ``` ##### Parallel ```bash time echo {1..5} |xargs -n 1 -P 5 sleep ``` a lot faster than ```bash time echo {1..5} |xargs -n1 sleep ``` ##### Copy all files from A to B ```bash 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 ```bash ls |xargs -n1 -I file sed -i '/^Pos/d' filename ``` ##### Add the file name to the first line of file ```bash ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt ``` ##### Count all files ```bash ls |xargs -n1 wc -l ``` ##### Turn output into a single line ```bash ls -l| xargs ``` ##### Count files within directories ```bash 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) ```bash cat requirements.txt| xargs -n1 sudo pip install ``` ##### Count lines in all file, also count total lines ```bash ls|xargs wc -l ``` ##### Xargs and grep ```bash cat grep_list |xargs -I{} grep {} filename ``` ## Find [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### List all sub directory/file in the current directory ```bash find . ``` ##### List all files under the current directory ```bash find . -type f ``` ##### List all directories under the current directory ```bash find . -type d ``` ##### Edit all files under current directory (e.g. replace 'www' with 'ww') ```bash find . name '*.php' -exec sed -i 's/www/w/g' {} \; ``` if no subdirectory ```bash replace "www" "w" -- * ``` //a space before * ##### Find and output only filename (e.g. "mso") ```bash find mso*/ -name M* -printf "%f\n" ``` ##### Find and delete file with size less than (e.g. 74 byte) ```bash find . -name "*.mso" -size -74c -delete ``` //M for MB, etc ## Loops [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### While loop, column subtraction of a file (e.g. a 3 columns file) ```bash while read a b c; do echo $(($c-$b));done < <(head filename) ``` //there is a space between the two '<'s ##### While loop, sum up column subtraction ```bash i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename) ``` ##### If loop ```bash if (($j==$u+2)) ``` //(( )) use for arithmetic operation ```bash if [[$age >21]] ``` //[[ ]] use for comparison ##### Test if file exist ```bash if [ -e 'filename' ] then echo -e "file exists!" fi ``` ##### For loop ```bash for i in $(ls); do echo file $i;done ``` ## Download [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Download all from a page ```bash wget -r -l1 -H -t1 -nd -N -np -A mp3 -e robots=off http://example.com ``` //-r: recursive and download all links on page //-l1: only one level link //-H: span host, visit other hosts //-t1: numbers of retries //-nd: don't make new directories, download to here //-N: turn on timestamp //-nd: no parent //-A: type (seperate by ,) //-e robots=off: ignore the robots.txt file which stop wget from crashing the site, sorry example.com ##### Upload a file to web and download (https://transfer.sh/) --> upload: ```bash curl --upload-file ./filename.txt https://transfer.sh/filename.txt ``` (the above command will return a URL, e.g: https://transfer.sh/tG8rM/filename.txt) --> download: ```bash curl https://transfer.sh/tG8rM/filename.txt -o filename.txt ``` ##### Download file if necessary ```bash data=file.txt url=http://www.example.com/$data if [! -s $data];then echo "downloading test data..." wget $url fi ``` ##### Wget to a filename (when a long name) ```bash wget -O filename "http://example.com" ``` ##### Wget files to a folder ```bash wget -P /path/to/directory "http://example.com" ``` ## Random [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Random pick 100 lines from a file ```bash shuf -n 100 filename ``` ##### Random order (lucky draw) ```bash 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) ```bash shuf -i 0-100 -n 15 ``` ##### Echo a random number ```bash echo $RANDOM ``` ##### Random from 0-9 ```bash echo $((RANDOM % 10)) ``` ##### Random from 1-10 ```bash echo $(((RANDOM %10)+1)) ``` ## Xwindow X11 GUI applications! Here are some GUI tools for you if you get bored by the text-only environment. ##### Enable X11 forwarding,in order to use graphical application on servers ```bash ssh -X user_name@ip_address ``` or setting through xhost --> Install the following for Centos: xorg-x11-xauth xorg-x11-fonts-* xorg-x11-utils ##### Little xwindow tools ```bash xclock xeyes ``` ##### Open pictures/images from ssh server ```bash 1. ssh -X user_name@ip_address 2. apt-get install eog 3. eog picture.png ``` ##### Use gedit on server (GUI editor) ```bash 1. ssh -X user_name@ip_address 2. apt-get install gedit 3. gedit filename.txt ``` ##### Open PDF file from ssh server ```bash 1. ssh -X user_name@ip_address 2. apt-get install evince 3. evince filename.pdf ``` ##### Use google-chrome browser from ssh server ```bash 1. ssh -X user_name@ip_address 2. apt-get install libxss1 libappindicator1 libindicator7 3. wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb 4. sudo apt-get install -f 5. dpkg -i google-chrome*.deb 6. google-chrome ``` [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ## Others [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Remove newline / nextline ```bash tr --delete '\n' output.txt ``` ##### Replace newline ```bash tr '\n' ' ' log & ``` or ```bash some_commands 2>log & ``` or ```bash some_commands 2>&1| tee logfile ``` or ```bash some_commands 2>&1 >>outfile ``` //0: standard input; 1: standard output; 2: standard error ##### Send mail ```bash echo 'heres the content'| mail -A 'file.txt' -s 'mail.subject' me@gmail.com ``` //use -a flag to set send from (-a "From: some@mail.tld") ##### .xls to csv ```bash xls2csv filename ``` ##### Append to file (e.g. hihi) ```bash echo 'hihi' >>filename ``` ##### Make BEEP sound ```bash speaker-test -t sine -f 1000 -l1 ``` ##### Set beep duration ```bash (speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid ``` ##### History edit/ delete ```bash ~/.bash_history ``` or ```bash history -d [line_number] ``` ##### Get last history/record filename ```bash head !$ ``` ##### Clean screen ```bash clear ``` or ```bash Ctrl+l ``` ##### Send data to last edited file ```bash cat /directory/to/file echo 100>!$ ``` ##### Run history number (e.g. 53) ```bash !53 ``` ##### Run last command ```bash !! ``` ##### Run last command that began with (e.g. cat filename) ```bash !cat ``` or ```bash !c ``` //run cat filename again ##### Extract .xf 1.unxz filename.tar.xz 2.tar -xf filename.tar ##### Install python package ```bash pip install packagename ``` ##### Delete current bash command ```bash Ctrl+U ``` or ```bash Ctrl+C ``` or ```bash Alt+Shift+# ``` //to make it to history ##### Add something to history (e.g. "addmetohistory") ```bash #addmetodistory ``` //just add a "#" before~~ ##### Sleep awhile or wait for a moment or schedule a job ```bash sleep 5;echo hi ``` ##### Count the time for executing a command ```bash time echo hi ``` ##### Backup with rsync ```bash rsync -av filename filename.bak rsync -av directory directory.bak rsync -av --ignore_existing directory/ directory.bak rsync -av --update directory directory.bak ``` //skip files that are newer on receiver (i prefer this one!) ##### Make all directories at one time! ```bash 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) ```bash cd tmp/ && tar xvf ~/a.tar ``` ##### Run command only if another command returns non-zero exit status (not finish) ```bash cd tmp/a/b/c ||mkdir -p tmp/a/b/c ``` ##### Extract to a path ```bash tar xvf -C /path/to/directory filename.gz ``` ##### Use backslash "\" to break long command ```bash cd tmp/a/b/c \ > || \ >mkdir -p tmp/a/b/c ``` ##### Get pwd ```bash VAR=$PWD; cd ~; tar xvf -C $VAR file.tar ``` //PWD need to be capital letter ##### List file type of file (e.g. /tmp/) ```bash file /tmp/ ``` //tmp/: directory ##### Bash script ```bash #!/bin/bash file=${1#*.} ``` //remove string before a "." ```bash file=${1%.*} ``` //remove string after a "." ##### Search from history ```bash Ctrl+r ``` ##### Python simple HTTP Server ```bash python -m SimpleHTTPServer ``` ##### Variables ```bash {i/a/,} ``` e.g. replace all ```bash {i//a/,} ``` //for variable i, replace all 'a' with a comma ##### Read user input ```bash read input echo $input ``` ##### Generate sequence 1-10 ```bash seq 10 ``` ##### Sum up input list (e.g. seq 10) ```bash seq 10|paste -sd+|bc ``` ##### Find average of input list/file ```bash i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc ``` ##### Generate all combination (e.g. 1,2) ```bash echo {1,2}{1,2} ``` //1 1, 1 2, 2 1, 2 2 ##### Generate all combination (e.g. A,T,C,G) ```bash 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 ```bash foo=$( $(basename filename.gz .gz).unpacked ``` ##### Use the squeeze repeat option (e.g. /t/t --> /t) ```bash tr -s "/t" < filename ``` ##### Do not print nextline with echo ```bash echo -e 'text here \c' ``` ##### Use the last argument ```bash !$ ``` ##### Check last exit code ```bash echo $? ``` ##### View first 50 characters of file ```bash head -c 50 file ``` ##### Group/combine rows into one row e.g. AAAA BBBB CCCC DDDD ```bash cat filename|paste - - --> AAAABBBB CCCCDDDD cat filename|paste - - - - --> AAAABBBBCCCCDDDD ``` ##### Fastq to fasta ```bash cat file.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' >file.fa ``` ##### Cut and get last column ```bash cat file|rev | cut -d/ -f1 | rev ``` ##### Add one to variable/increment a numeric variable (e.g. $var) ```bash ((var++)) ``` ##### Some handy environment variables $0 :name of shell or shell script. $1, $2, $3, ... :positional parameters. $# :number of positional parameters. $? :most recent foreground pipeline exit status. $- :current options set for the shell. $$ :pid of the current shell (not subshell). $! :is the PID of the most recent background command. ##### Clear the contents of a file (e.g. filename) ```bash >filename ``` ##### Unzip tar.bz2 file (e.g. file.tar.bz2) ```bash tar xvfj file.tar.bz2 ``` ##### Output a y/n repeatedly until killed 'y': ```bash yes ``` or 'n': ```bash yes n ``` or 'anything': ```bash yes anything ``` For example: ```bash yes | rm -r large_directory ``` ##### Create dummy file of certain size instantly (e.g. 200mb) ```bashdd if=/dev/zero of=//dev/shm/200m bs=1024k count=200 ``` Standard output: 200+0 records in 200+0 records out 209715200 bytes (210 MB) copied, 0.0955679 s, 2.2 GB/s ## System [[back to top](#handy-bash-oneliner-commands-for-tsv-file-editing)] ##### Snapshot of the current processes ```bash ps ``` ##### Check graphics card ```bash lspci ``` ##### Show IP address ```bash $ip add show ``` or ```bash ifconfig ``` ##### Check system version ```bash cat /etc/*-release ``` ##### Linux Programmer's Manuel: hier- description of the filesystem hierarchy ```bash man hier ``` ##### List job ```bash jobs -l ``` ##### Export PATH ```bash export PATH=$PATH:~/path/you/want ``` ##### Make file execuable ```bash chmod +x filename ``` //you can now ./filename to execute it ##### List screen ```bash screen -d -r ``` ##### Echo screen name ```bash screen -ls ``` ##### Check system (x86-64) ```bash uname -i ``` ##### Surf the net ```bash links www.google.com ``` ##### Add user, set passwd ```bash useradd username passwd username ``` ##### Edit variable for bash, (e.g. displaying the whole path) ```bash 1. joe ~/.bash_profile 2. export PS1='\u@\h:\w\$' ``` //$PS1 is a variable that defines the makeup and style of the command prompt ```bash 3. source ~/.bash_profile ``` ##### Edit environment setting (e.g. alias) ```bash 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) ```bash $echo $PATH ``` //list of directories separated by a colon ##### List all environment variables for current user ```bash $env ``` ##### Show partition format ```bash lsblk ``` ##### Soft link program to bin ```bash ln -s /path/to/program /home/usr/bin ``` //must be the whole path to the program ##### Show hexadecimal view of data ```bash hexdump -C filename.class ``` ##### Jump to different node ```bash rsh node_name ``` ##### Check port (active internet connection) ```bash netstat -tulpn ``` ##### Find whick link to a file ```bash readlink filename ``` ##### Check where a command link to (e.g. python) ```bash which python ``` ##### List total size of a directory ```bash du -hs . ``` or ```bash du -sb ``` ##### Copy directory with permission setting ```bash cp -rp /path/to/directory ``` ##### Store current directory ```bash pushd . $popd ;dirs -l ``` ##### Show disk usage ```bash df -h ``` or ```bash du -h ``` or ```bash du -sk /var/log/* |sort -rn |head -10 ``` ##### Show current runlevel ```bash runlevel ``` ##### Switch runlevel ```bash init 3 ``` or ```bash telinit 3 ``` ##### Permanently modify runlevel ```bash 1. edit /etc/init/rc-sysinit.conf 2. env DEFAULT_RUNLEVEL=2 ``` ##### Become root ```bash su ``` ##### Become somebody ```bash su somebody ``` ##### Report user quotes on device ```bash requota -auvs ``` ##### Get entries in a number of important databases ```bash getent database_name ``` (e.g. the 'passwd' database) ```bash getent passwd ``` //list all user account (all local and LDAP) (e.g. fetch list of grop accounts) ```bash getent group ``` //store in database 'group' ##### Change owner of file ```bash chown user_name filename chown -R user_name /path/to/directory/ ``` //chown user:group filename ##### List current mount detail ```bash df ``` ##### List current usernames and user-numbers ```bash cat /etc/passwd ``` ##### Get all username ```bash getent passwd| awk '{FS="[:]"; print $1}' ``` ##### Show all users ```bash compgen -u ``` ##### Show all groups ```bash compgen -g ``` ##### Show group of user ```bash group username ``` ##### Show uid, gid, group of user ```bash id username ``` ##### Check if it's root ```bash if [$(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 ```bash more /proc/cpuinfo ``` or ```bash lscpu ``` ##### Set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120) ```bash setquota username 120586240 125829120 0 0 /home ``` ##### Show quota for user ```bash quota -v username ``` ##### Fork bomb ```bash :(){:|:&};: ``` //dont try this at home ##### Check user login ```bash lastlog ``` ##### Edit path for all users ```bash joe /etc/environment ``` //edit this file ##### Show running processes ```bash ps aux ``` ##### Find maximum number of processes ```bash cat /proc/sys/kernal/pid_max ``` ##### Show and set user limit ```bash ulimit -u ``` ##### Which ports are listening for TCP connections from the network ```bash nmap -sT -O localhost ``` ##### Print out number of cores/ processors ```bash nproc --all ``` ##### Check status of each core 1. top 2. press '1' ##### Show jobs and PID ```bash jobs -l ``` ##### List all running services ```bash service --status-all ``` ##### Schedule shutdown server ```bash shutdown -r +5 "Server will restart in 5 minutes. Please save your work." ``` ##### Cancel scheduled shutdown ```bash shutdown -c ``` ##### Boardcast to all users ```bash wall -n hihi ``` ##### Kill all process of a user ```bash pkill -U user_name ``` ##### Set gedit preference on server -->you might have to install the following: apt-get install libglib2.0-bin; yum install dconf dconf-editor; yum install dbus dbus-x11; -->Check list ```bash gsettings list-recursively ``` -->Change setting e.g. ```bash gsettings set org.gnome.gedit.preferences.editor highlight-current-line true gsettings set org.gnome.gedit.preferences.editor scheme 'cobalt' gsettings set org.gnome.gedit.preferences.editor use-default-font false gsettings set org.gnome.gedit.preferences.editor editor-font 'Cantarell Regular 12' ``` ##### Find out who has logged in on your system --> [Quick] Printing out only the names: ```bash users ``` --> [Detail] Printing out login time, load average, etc ```bash w ``` ##### Add user to a group (e.g add user 'nice' to the group 'docker', so that he can run docker without sudo) ```bash sudo gpasswd -a nice docker ``` ##### pip install python package without root ```bash 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...) ```bash 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 ``` =-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-