Bash-Oneliner/README.md

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# Bash-Oneliner
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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.
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This blog will focus on simple bash commands for parsing data; some of them are for Linux system maintenance. I apologize that there are no detailed citation for all the commands, but they are probably from dear Google and Stackoverflow.
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English and bash are not my first language, so... correct me anytime, thank you!
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And if you know any cool command that are not included here, Please Teach Me.
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In case you would like to check and vote up my questions on Stackoverflow, here's my page:
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http://stackoverflow.com/users/4290753/once
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Here's a more stylish version of Bash-Oneliner~
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http://onceupon.github.io/Bash-Oneliner/
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## Handy Bash oneliner commands
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- [Grep](#grep)
- [Sed](#sed)
- [Awk](#awk)
- [Xargs](#xargs)
- [Find](#find)
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- [Loops](#loops)
- [Variable](#variable)
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- [Math](#math)
- [Time](#time)
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- [Download](#download)
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- [Random](#random)
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- [Xwindow](#xwindow)
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- [System](#system)
- [Hardware](#hardware)
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- [Others](#others)
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## Grep
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##### Grep only IP address
```bash
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grep -Eo '[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}'
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```
##### Grep string starting with (e.g. 'S')
```bash
grep -o 'S.*'
```
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##### Extract text bewteen words (e.g. w1,w2)
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```bash
grep -o -P '(?<=w1).*(?=w2)'
```
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##### Grep only integer
```bash
grep -o '[0-9]*'
```
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##### Grep lines without word (e.g. bbo)
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```bash
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grep -v bbo filename
```
##### Grep lines not begin with string (e.g. #)
```bash
grep -v '^#' file.txt
```
##### Grep variables with space within it (e.g. bbo="some strings")
```bash
grep "$boo" filename
```
#remember to quote the variable!
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##### Grep only one/first match (e.g. bbo)
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```bash
grep -m 1 bbo filename
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```
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##### Grep and count (e.g. bbo)
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```bash
grep -c bbo filename
```
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##### Insensitive grep (e.g. bbo/BBO/Bbo)
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```bash
grep -i "bbo" filename
```
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##### Count occurrence (e.g. three times a line count three times)
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```bash
grep -o bbo filename
```
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##### COLOR the match (e.g. bbo)!
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```bash
grep --color bbo filename
```
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##### Grep search all files in a directory(e.g. bbo)
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```bash
grep -R bbo /path/to/directory
```
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or
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```bash
grep -r bbo /path/to/directory
```
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##### Search all files in directory, only output file names with matches(e.g. bbo)
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```bash
grep -Rh bbo /path/to/directory
```
or
```bash
grep -rh bbo /path/to/directory
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```
or only list filename with match
```bash
grep -rl bbo /path/to/directory
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```
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##### Grep OR (e.g. A or B or C or D)
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```
grep 'A\|B\|C\|D'
```
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##### Grep AND (e.g. A and B)
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```bash
grep 'A.*B'
```
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##### Grep all content of a fileA from fileB
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```bash
grep -f fileA fileB
```
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##### Grep a tab
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```bash
grep $'\t'
```
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##### Grep variable from variable
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```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 []!
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```
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##### Grep strings between a bracket()
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```bash
grep -oP '\(\K[^\)]+'
```
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##### Grep number of characters with known strings in between(e.g. AAEL000001-RA)
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```bash
grep -o -w "\w\{10\}\-R\w\{1\}"
# \w word character [0-9a-zA-Z_] \W not word character
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```
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##### A lot examples here
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http://www.cyberciti.biz/faq/grep-regular-expressions/
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## Sed
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[[back to top](#handy-bash-oneliner-commands)]
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##### Remove the 1st line
```bash
sed 1d filename
```
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##### Remove the first 100 lines (remove line 1-100)
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```bash
sed 1,100d filename
```
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##### Remove lines with string (e.g. bbo)
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```bash
sed "/bbo/d" filename
- case insensitive:
sed "/bbo/Id" filename
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```
##### Remove lines whose nth character not equal to a value (e.g. 5th character not equal to 2)
```bash
sed -E '/^.{5}[^2]/d'
#aaaa2aaa (you can stay)
#aaaa1aaa (delete!)
```
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##### Edit infile (edit and save)
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```bash
sed -i "/bbo/d" filename
```
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##### When using variable (e.g. $i), use double quotes " "
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e.g. add >$i to the first line (to make a FASTA file)
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```bash
sed "1i >$i"
# notice the double quotes! in other examples, you can use a single quote, but here, no way!
# '1i' means insert to first line
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```
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##### Delete/remove empty lines
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```bash
sed '/^\s*$/d'
```
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or
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```bash
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sed '/^$/d'
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```
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##### Delete/remove last line
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```bash
sed '$d'
```
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##### Delete/remove last character from end of file
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```bash
sed -i '$ s/.$//' filename
```
##### Add string to beginning of file (e.g. "\[")
```bash
sed -i '1s/^/[/' file
```
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##### Add string to end of file (e.g. "]")
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```bash
sed '$s/$/]/' filename
```
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##### Add newline to the end
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```bash
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sed '$a\'
```
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##### Add string to beginning of every line (e.g. bbo)
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```bash
sed -e 's/^/bbo/' file
```
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##### Add string to end of each line (e.g. "}")
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```bash
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sed -e 's/$/\}\]/' filename
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```
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##### Add \n every nth character (e.g. every 4th character)
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```bash
sed 's/.\{4\}/&\n/g'
```
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##### Concatenate/combine/join files with a seperator and next line (e.g seperate by ",")
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```bash
sed -s '$a,' *.json > all.json
```
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##### Substitution (e.g. replace A by B)
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```bash
sed 's/A/B/g' filename
```
##### Substitution with wildcard (e.g. replace a line start with aaa= by aaa=/my/new/path)
```bash
sed "s/aaa=.*/aaa=\/my\/new\/path/g"
```
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##### Select lines start with string (e.g. bbo)
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```bash
sed -n '/^@S/p'
```
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##### Delete lines with string (e.g. bbo)
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```bash
sed '/bbo/d' filename
```
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##### Print/get/trim a range of line (e.g. line 500-5000)
```bash
sed -n 500,5000p filename
```
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##### Print every nth lines
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```bash
sed -n '0~3p' filename
# catch 0: start; 3: step
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```
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##### Print every odd # lines
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```bash
sed -n '1~2p'
```
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##### Print every third line including the first line
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```bash
sed -n '1p;0~3p'
```
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##### Remove leading whitespace and tabs
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```bash
sed -e 's/^[ \t]*//'
```
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//notice a whitespace before '\t'!!
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##### Remove only leading whitespace
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```bash
sed 's/ *//'
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# notice a whitespace before '*'!!
```
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##### Remove ending commas
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```bash
sed 's/,$//g'
```
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##### Add a column to the end
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```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
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```
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```bash
for i in $(ls);do sed -i "s/$/\t$i/" $i;done
```
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##### Add extension of filename to last column
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```bash
for i in T000086_1.02.n T000086_1.02.p;do sed "s/$/\t${i/*./}/" $i;done >T000086_1.02.np
```
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##### Remove newline\ nextline
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```bash
sed ':a;N;$!ba;s/\n//g'
```
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##### Print a particular line (e.g. 123th line)
```bash
sed -n -e '123p'
```
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##### Print a number of lines (e.g. line 10th to line 33 rd)
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```bash
sed -n '10,33p' <filename
```
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##### Change delimiter
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```bash
sed 's=/=\\/=g'
```
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##### Replace with wildcard (e.g A-1-e or A-2-e or A-3-e....)
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```bash
sed 's/A-.*-e//g' filename
```
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##### Remove last character of file
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```bash
sed '$ s/.$//'
```
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##### Insert character at specified position of file (e.g. AAAAAA --> AAA#AAA)
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```bash
sed -r -e 's/^.{3}/&#/' file
```
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## Awk
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[[back to top](#handy-bash-oneliner-commands)]
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##### Set tab as field separator
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```bash
awk -F $'\t'
```
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##### Output as tab separated (also as field separator)
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```bash
awk -v OFS='\t'
```
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##### Pass variable
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```bash
a=bbo;b=obb;
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awk -v a="$a" -v b="$b" "$1==a && $10=b" filename
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```
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##### Print line number and number of characters on each line
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```bash
awk '{print NR,length($0);}' filename
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```
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##### Find number of columns
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```bash
awk '{print NF}'
```
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##### Reverse column order
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```bash
awk '{print $2, $1}'
```
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##### Check if there is a comma in a column (e.g. column $1)
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```bash
awk '$1~/,/ {print}'
```
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##### Split and do for loop
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```bash
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awk '{split($2, a,",");for (i in a) print $1"\t"a[i]}' filename
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```
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##### Print all lines before nth occurence of a string (e.g stop print lines when bbo appears 7 times)
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```bash
awk -v N=7 '{print}/bbo/&& --N<=0 {exit}'
```
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##### Print filename and last line of all files in directory
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```bash
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ls|xargs -n1 -I file awk '{s=$0};END{print FILENAME,s}' file
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```
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##### Add string to the beginning of a column (e.g add "chr" to column $3)
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```bash
awk 'BEGIN{OFS="\t"}$3="chr"$3'
```
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##### Remove lines with string (e.g. bbo)
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```bash
awk '!/bbo/' file
```
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##### Remove last column
```bash
awk 'NF{NF-=1};1' file
```
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##### Usage and meaning of NR and FNR
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e.g.
fileA:
a
b
c
fileB:
d
e
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```bash
awk 'print FILENAME, NR,FNR,$0}' fileA fileB
```
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fileA 1 1 a
fileA 2 2 b
fileA 3 3 c
fileB 4 1 d
fileB 5 2 e
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##### AND gate
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e.g.
fileA:
1 0
2 1
3 1
4 0
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fileB:
1 0
2 1
3 0
4 1
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```bash
awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB
```
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1 0
2 1
3 0
4 0
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##### Round all numbers of file (e.g. 2 significant figure)
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```bash
awk '{while (match($0, /[0-9]+\[0-9]+/)){
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\printf "%s%.2f", substr($0,0,RSTART-1),substr($0,RSTART,RLENGTH)
\$0=substr($0, RSTART+RLENGTH)
\}
\print
\}'
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```
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##### Give number/index to every row
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```bash
awk '{printf("%s\t%s\n",NR,$0)}'
```
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##### Break combine column data into rows
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e.g.
seperate
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David cat,dog
into
David cat
David dog
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2016-08-18 03:03:45 +00:00
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
```
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##### Average a file (each line in file contains only one number)
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```bash
awk '{s+=$1}END{print s/NR}'
```
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##### Print field start with string (e.g Linux)
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```bash
awk '$1 ~ /^Linux/'
```
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##### Sort a row (e.g. 1 40 35 12 23 --> 1 12 23 35 40)
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```bash
awk ' {split( $0, a, "\t" ); asort( a ); for( i = 1; i <= length(a); i++ ) printf( "%s\t", a[i] ); printf( "\n" ); }'
```
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##### Subtract previous row values (add column6 which equal to column4 minus last column5)
```bash
awk '{$6 = $4 - prev5; prev5 = $5; print;}'
```
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## Xargs
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[[back to top](#handy-bash-oneliner-commands)]
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##### Set tab as delimiter (default:space)
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```bash
xargs -d\t
```
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##### Display 3 items per line
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```bash
echo 1 2 3 4 5 6| xargs -n 3
# 1 2 3
# 4 5 6
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```
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##### Prompt before execution
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```bash
echo a b c |xargs -p -n 3
```
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##### Print command along with output
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```bash
xargs -t abcd
# bin/echo abcd
# abcd
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```
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##### With find and rm
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```bash
find . -name "*.html"|xargs rm -rf
```
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##### Delete fiels with whitespace in filename (e.g. "hello 2001")
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```bash
find . -name "*.c" -print0|xargs -0 rm -rf
```
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##### Show limits
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```bash
xargs --show-limits
```
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##### Move files to folder
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```bash
find . -name "*.bak" -print 0|xargs -0 -I {} mv {} ~/old
```
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or
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```bash
find . -name "*.bak" -print 0|xargs -0 -I file mv file ~/old
```
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##### Move first 100th files to a directory (e.g. d1)
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```bash
ls |head -100|xargs -I {} mv {} d1
```
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##### Parallel
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```bash
time echo {1..5} |xargs -n 1 -P 5 sleep
```
a lot faster than
```bash
time echo {1..5} |xargs -n1 sleep
```
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##### Copy all files from A to B
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```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)
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```
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##### With sed
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```bash
ls |xargs -n1 -I file sed -i '/^Pos/d' filename
```
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##### Add the file name to the first line of file
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```bash
ls |sed 's/.txt//g'|xargs -n1 -I file sed -i -e '1 i\>file\' file.txt
```
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##### Count all files
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```bash
ls |xargs -n1 wc -l
```
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##### Turn output into a single line
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```bash
ls -l| xargs
```
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##### Count files within directories
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```bash
echo mso{1..8}|xargs -n1 bash -c 'echo -n "$1:"; ls -la "$1"| grep -w 74 |wc -l' --
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# "--" signals the end of options and display further option processing
```
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##### Download dependencies files and install (e.g. requirements.txt)
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```bash
cat requirements.txt| xargs -n1 sudo pip install
```
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##### Count lines in all file, also count total lines
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```bash
ls|xargs wc -l
```
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##### Xargs and grep
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```bash
cat grep_list |xargs -I{} grep {} filename
```
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##### Xargs and sed (replace all old ip address with new ip address under /etc directory)
```bash
grep -rl '192.168.1.111' /etc | xargs sed -i 's/192.168.1.111/192.168.2.111/g'
```
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## Find
2018-04-12 06:15:22 +00:00
[[back to top](#handy-bash-oneliner-commands)]
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##### List all sub directory/file in the current directory
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```bash
find .
```
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##### List all files under the current directory
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```bash
find . -type f
```
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##### List all directories under the current directory
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```bash
find . -type d
```
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##### Edit all files under current directory (e.g. replace 'www' with 'ww')
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```bash
find . name '*.php' -exec sed -i 's/www/w/g' {} \;
```
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if no subdirectory
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```bash
replace "www" "w" -- *
# a space before *
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```
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##### Find and output only filename (e.g. "mso")
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```bash
find mso*/ -name M* -printf "%f\n"
```
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##### Find and delete file with size less than (e.g. 74 byte)
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```bash
find . -name "*.mso" -size -74c -delete
# M for MB, etc
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```
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## Loops
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[[back to top](#handy-bash-oneliner-commands)]
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##### While loop, column subtraction of a file (e.g. a 3 columns file)
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```bash
while read a b c; do echo $(($c-$b));done < <(head filename)
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#there is a space between the two '<'s
```
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##### While loop, sum up column subtraction
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```bash
i=0; while read a b c; do ((i+=$c-$b)); echo $i; done < <(head filename)
```
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##### While loop, 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')
```bash
while [[ $(pidof perl) ]];do echo f;sleep 10;done && python timetorunpython.py
```
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##### If loop
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```bash
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# if and else loop for string matching
if [[ "$c" == "read" ]]; then outputdir="seq"; else outputdir="write" ; fi
```
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if (($j==$u+2))
#(( )) use for arithmetic operation
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```
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```bash
if [[$age >21]]
#[[ ]] use for comparison
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```
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##### Test if file exist
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```bash
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if [ -e 'filename' ]
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then
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echo -e "file exists!"
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fi
```
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##### if else Test if file exist
```bash
if [ -e $filename ]; then echo -e "file exists!"; else mkdir $filename; fi
```
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##### For loop
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```bash
for i in $(ls); do echo file $i;done
```
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##### for loop, press any key to continue each loop
```bash
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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
```
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##### for loop, print a file line by line when a key is pressed
```bash
for line in $(cat myfile); do echo $line; read -n1; done
```
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##### switch (case in bash)
```bash
read type;
case $type in
'0')
echo 'how'
;;
'1')
echo 'are'
;;
'2')
echo 'you'
;;
esac
```
## Variable
2018-04-12 06:15:22 +00:00
[[back to top](#handy-bash-oneliner-commands)]
##### variable substitution within quotes
```bash
# foo=bar
echo "'$foo'"
#'bar'
# double/single quotes around single quotes make the inner single quotes expand variables
```
##### get the length of variable
```bash
var="some string"
echo ${#var}
# 11
```
##### get the first character of the variable
```bash
var="some string"
echo ${var%%"${var#?}"}
#s
```
##### remove the first or last string from variable
```bash
var="some string"
echo ${var:2}
#me string
```
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##### replacement (e.g. remove the first leading 0 )
```bash
var="0050"
echo ${var[@]#0}
#050
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```
##### replacement (e.g. replace 'a' with ',')
```bash
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{var/a/,}
```
##### replace all (e.g. replace all 'a' with ',')
```bash
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{var//a/,}
```
```bash
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#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)
```bash
var=HelloWorld
echo ${var,,}
helloworld
```
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## Math
2018-04-12 06:16:31 +00:00
[[back to top](#handy-bash-oneliner-commands)]
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##### Print out the prime factors of a number (e.g. 50)
```bash
factor 50
```
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##### Sum up input list (e.g. seq 10)
```bash
seq 10|paste -sd+|bc
```
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##### Sum up a file (each line in file contains only one number)
```bash
awk '{s+=$1} END {print s}' filename
```
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##### Column subtraction
```bash
cat file| awk -F '\t' 'BEGIN {SUM=0}{SUM+=$3-$2}END{print SUM}'
```
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##### Simple math with expr
```bash
expr 10+20 #30
expr 10\*20 #600
expr 30 \> 20 #1 (true)
```
##### More math with bc
- Number of decimal digit/ significant figure
```bash
echo "scale=2;2/3" | bc
#.66
```
- Exponent operator
```bash
echo "10^2" | bc
#100
```
- Using variables
```bash
echo "var=5;--var"| bc
#4
```
## Time
[[back to top](#handy-bash-oneliner-commands)]
##### Find out the time require for executing a command
```bash
time echo hi
```
##### Wait for some time (e.g 10s)
```bash
sleep 10
```
##### Log out your account after a certain period of time (e.g 10 seconds)
```bash
TMOUT=10
#once you set this variable, logout timer start running!
```
##### Set how long you want to run a command
```bash
#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)
```bash
at now + 1min #time-units can be minutes, hours, days, or weeks
warning: commands will be executed using /bin/sh
2018-04-18 03:30:24 +00:00
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
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[[back to top](#handy-bash-oneliner-commands)]
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##### Download all from a page
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```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
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```
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##### 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"
```
2016-06-16 06:44:57 +00:00
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2017-03-29 08:52:59 +00:00
## Random
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[[back to top](#handy-bash-oneliner-commands)]
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##### Random pick 100 lines from a file
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```bash
shuf -n 100 filename
```
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##### Random order (lucky draw)
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```bash
for i in a b c d e; do echo $i; done| shuf
```
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##### Echo series of random numbers between a range (e.g. shuffle numbers from 0-100, then pick 15 of them randomly)
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```bash
shuf -i 0-100 -n 15
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```
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##### Echo a random number
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```bash
echo $RANDOM
```
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##### Random from 0-9
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```bash
echo $((RANDOM % 10))
```
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##### Random from 1-10
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```bash
echo $(((RANDOM %10)+1))
```
2016-06-27 05:54:48 +00:00
2017-06-09 04:26:34 +00:00
## Xwindow
2018-04-12 06:15:22 +00:00
[[back to top](#handy-bash-oneliner-commands)]
2017-09-28 05:40:02 +00:00
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X11 GUI applications! Here are some GUI tools for you if you get bored by the text-only environment.
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##### Enable X11 forwarding,in order to use graphical application on servers
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```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
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##### Little xwindow tools
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```bash
xclock
xeyes
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xcowsay
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```
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##### Open pictures/images from ssh server
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```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
```
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##### Open PDF file from ssh server
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```bash
1. ssh -X user_name@ip_address
2. apt-get install evince
3. evince filename.pdf
```
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##### Use google-chrome browser from ssh server
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```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
```
## System
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[[back to top](#handy-bash-oneliner-commands)]
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##### Snapshot of the current processes
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```bash
ps
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```
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##### Check graphics card
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```bash
lspci
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```
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##### Show IP address
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```bash
$ip add show
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```
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or
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```bash
ifconfig
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```
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##### Check system version
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```bash
cat /etc/*-release
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```
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##### Linux Programmer's Manuel: hier- description of the filesystem hierarchy
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```bash
man hier
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```
##### List job
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```bash
jobs -l
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```
##### Export PATH
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```bash
export PATH=$PATH:~/path/you/want
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```
##### Make file execuable
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```bash
chmod +x filename
# you can now ./filename to execute it
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```
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##### Check system (x86-64)
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```bash
uname -i
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```
##### Surf the net
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```bash
links www.google.com
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```
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##### Add user, set passwd
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```bash
useradd username
passwd username
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```
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##### 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
```
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```bash
3. source ~/.bash_profile
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```
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##### Edit environment setting (e.g. alias)
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```bash
1. joe ~/.bash_profile
2. alias pd="pwd" //no more need to type that 'w'!
3. source ~/.bash_profile
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```
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##### List environment variables (e.g. PATH)
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```bash
$echo $PATH
# list of directories separated by a colon
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```
##### List all environment variables for current user
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```bash
$env
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```
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##### Show partition format
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```bash
lsblk
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```
##### Soft link program to bin
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```bash
ln -s /path/to/program /home/usr/bin
# must be the whole path to the program
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```
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##### Show hexadecimal view of data
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```bash
hexdump -C filename.class
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```
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##### Jump to different node
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```bash
rsh node_name
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```
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##### Check port (active internet connection)
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```bash
netstat -tulpn
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```
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##### Find which link to a file
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```bash
readlink filename
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```
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##### Check where a command link to (e.g. python)
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```bash
which python
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```
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##### List total size of a directory
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```bash
du -hs .
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```
or
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```bash
du -sb
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```
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##### Copy directory with permission setting
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```bash
cp -rp /path/to/directory
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```
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##### Store current directory
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```bash
pushd . $popd ;dirs -l
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```
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##### Show disk usage
```bash
df -h
```
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or
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```bash
du -h
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```
or
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```bash
du -sk /var/log/* |sort -rn |head -10
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```
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##### Show current runlevel
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```bash
runlevel
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```
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##### Switch runlevel
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```bash
init 3
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```
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or
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```bash
telinit 3
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```
##### Permanently modify runlevel
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```bash
1. edit /etc/init/rc-sysinit.conf
2. env DEFAULT_RUNLEVEL=2
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```
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##### Become root
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```bash
su
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```
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##### Become somebody
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```bash
su somebody
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```
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##### Report user quotes on device
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```bash
requota -auvs
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```
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##### Get entries in a number of important databases
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```bash
getent database_name
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```
(e.g. the 'passwd' database)
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```bash
getent passwd
# list all user account (all local and LDAP)
# (e.g. fetch list of grop accounts)
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```
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```bash
getent group
# store in database 'group'
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```
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##### Change owner of file
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```bash
chown user_name filename
chown -R user_name /path/to/directory/
# chown user:group filename
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```
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##### List current mount detail
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```bash
df
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```
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##### List current usernames and user-numbers
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```bash
cat /etc/passwd
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```
##### Get all username
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```bash
getent passwd| awk '{FS="[:]"; print $1}'
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```
##### Show all users
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```bash
compgen -u
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```
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##### Show all groups
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```bash
compgen -g
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```
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##### Show group of user
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```bash
group username
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```
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##### Show uid, gid, group of user
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```bash
id username
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```
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##### Check if it's root
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```bash
if [$(id -u) -ne 0];then
echo "You are not root!"
exit;
fi
# 'id -u' output 0 if it's not root
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```
##### Find out CPU information
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```bash
more /proc/cpuinfo
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```
or
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```bash
lscpu
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```
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##### Set quota for user (e.g. disk soft limit: 120586240; hard limit: 125829120)
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```bash
setquota username 120586240 125829120 0 0 /home
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```
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##### Show quota for user
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```bash
quota -v username
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```
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##### Fork bomb
# dont try this at home
```bash
:(){:|:&};:
```
##### Check user login
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```bash
lastlog
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```
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##### Edit path for all users
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```bash
joe /etc/environment
# edit this file
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```
##### Show running processes
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```bash
ps aux
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```
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##### Find maximum number of processes
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```bash
cat /proc/sys/kernal/pid_max
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```
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##### Show and set user limit
```bash
ulimit -u
```
##### Which ports are listening for TCP connections from the network
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```bash
nmap -sT -O localhost
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#notice that some commpanies might not like you using nmap
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```
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##### Print out number of cores/ processors
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```bash
nproc --all
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```
##### Check status of each core
1. top
2. press '1'
##### Show jobs and PID
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```bash
jobs -l
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```
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##### List all running services
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```bash
service --status-all
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```
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##### Schedule shutdown server
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```bash
shutdown -r +5 "Server will restart in 5 minutes. Please save your work."
2016-09-02 03:56:37 +00:00
```
##### Cancel scheduled shutdown
```bash
shutdown -c
```
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##### Boardcast to all users
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```bash
wall -n hihi
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```
##### Kill all process of a user
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```bash
pkill -U user_name
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```
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##### Kill all process of a program
```bash
kill -9 $(ps aux | grep 'program_name' | awk '{print $2}')
```
##### Set gedit preference on server
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-->you might have to install the following:
apt-get install libglib2.0-bin;
yum install dconf dconf-editor;
yum install dbus dbus-x11;
-->Check list
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```bash
gsettings list-recursively
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```
-->Change setting
e.g.
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```bash
gsettings set org.gnome.gedit.preferences.editor highlight-current-line true
gsettings set org.gnome.gedit.preferences.editor scheme 'cobalt'
gsettings set org.gnome.gedit.preferences.editor use-default-font false
gsettings set org.gnome.gedit.preferences.editor editor-font 'Cantarell Regular 12'
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```
##### Find out who has logged in on your system
--> [Quick] Printing out only the names:
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```bash
users
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```
--> [Detail] Printing out login time, load average, etc
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```bash
w
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```
##### Add user to a group (e.g add user 'nice' to the group 'docker', so that he can run docker without sudo)
```bash
sudo gpasswd -a nice docker
```
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##### pip install python package without root
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```bash
1. pip install --user package_name
2. You might need to export ~/.local/bin/ to PATH: export PATH=$PATH:~/.local/bin/
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```
##### Removing old linux kernels (when /boot almost full...)
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```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
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```
##### Change hostname
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```bash
sudo hostname your-new-name
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```
if not working, do also:
```bash
hostnamectl set-hostname your-new-hostname
```
then run:
hostnamectl
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check /etc/hostname
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if still not working..., edit:
/etc/sysconfig/network
/etc/sysconfig/network-scripts/ifcfg-ensxxx
add HOSTNAME="your-new-hostname"
##### List installed packages
```bash
apt list --installed
```
or Red Hat:
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```bash
yum list installed
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```
##### Check which file make the device busy on umount
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```bash
lsof /mnt/dir
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```
##### When sound not working
```bash
killall pulseaudio
```
then press Alt-F2 and type in pulseaudio
##### When sound not working
```bash
killall pulseaudio
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```
##### List information about SCSI devices
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```bash
lsscsi
```
##### Tutorial for setting up your own DNS server
http://onceuponmine.blogspot.tw/2017/08/set-up-your-own-dns-server.html
2017-09-08 01:22:48 +00:00
##### Tutorial for creating a simple daemon
http://onceuponmine.blogspot.tw/2017/07/create-your-first-simple-daemon.html
2017-09-08 01:22:48 +00:00
##### Tutorial for using your gmail to send email
http://onceuponmine.blogspot.tw/2017/10/setting-up-msmtprc-and-use-your-gmail.html
##### 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)
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```bash
telnet 192.168.2.106 53
```
##### change network maximum transmission unit (mtu) (e.g. change to 9000)
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```bash
ifconfig eth0 mtu 9000
```
##### get pid of a running process (e.g python)
```bash
pidof python
```
or
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```bash
ps aux|grep python
```
##### ntp
start ntp:
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```bash
ntpd
```
check ntp:
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```bash
ntpq -p
```
##### remove unnecessary files to clean your server
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```bash
sudo apt-get autoremove
sudo apt-get clean
sudo rm -rf ~/.cache/thumbnails/*
```
Remove old kernal:
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```bash
sudo dpkg --list 'linux-image*'
sudo apt-get remove linux-image-OLDER_VERSION
```
2017-09-28 05:28:23 +00:00
##### Increase/ resize root partition (root partition is an LVM logical volume)
2017-09-28 05:28:23 +00:00
```bash
pvscan
lvextend -L +130G /dev/rhel/root -r
```
#Adding -r will grow filesystem after resizing the volume.
2017-09-28 05:28:23 +00:00
2017-09-28 10:10:55 +00:00
##### Create a UEFI Bootable USB drive (e.g. /dev/sdc1)
```bash
sudo dd if=~/path/to/isofile.iso of=/dev/sdc1 oflag=direct bs=1048576
```
##### Locate and remove a package
```bash
sudo dpkg -l | grep <package_name>
sudo dpkg --purge <package_name>
```
##### Create a ssh tunnel
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```bash
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.
2017-11-29 06:00:46 +00:00
```
##### Get process ID of a process (e.g. sublime_text)
```bash
#pidof
pidof sublime_text
#pgrep, you dont have to type the whole program name
pgrep sublim
#top, takes longer time
top|grep sublime_text
```
2018-04-27 08:09:36 +00:00
##### Some benchmarking tools for your server
2018-04-27 09:01:11 +00:00
[aio-stress](https://openbenchmarking.org/test/pts/aio-stress) - AIO benchmark.
[bandwidth](https://zsmith.co/bandwidth.html) - memory bandwidth benchmark.
[bonnie++](https://www.coker.com.au/bonnie++/) - hard drive and file system performance benchmark.
[dbench](https://dbench.samba.org/) - generate I/O workloads to either a filesystem or to a networked CIFS or NFS server.
[dnsperf](https://www.dnsperf.com/) - authorative and recursing DNS servers.
[filebench](https://github.com/filebench/filebench) - model based file system workload generator.
[fio](https://linux.die.net/man/1/fio) - I/O benchmark.
[fs_mark](https://github.com/josefbacik/fs_mark) - synchronous/async file creation benchmark.
[httperf](https://github.com/httperf/httperf) - measure web server performance.
[interbench](https://github.com/ckolivas/interbench) - linux interactivity benchmark.
[ioblazer](https://labs.vmware.com/flings/ioblazer) - multi-platform storage stack micro-benchmark.
[iozone](http://www.iozone.org/) - filesystem benchmark.
2018-04-27 09:01:52 +00:00
[iperf3](https://iperf.fr/iperf-download.php) - measure TCP/UDP/SCTP performance.
2018-04-27 09:01:11 +00:00
[kcbench](https://github.com/knurd/kcbench) - kernel compile benchmark, compiles a kernel and messures the time it takes.
[lmbench](http://www.bitmover.com/lmbench/) - Suite of simple, portable benchmarks.
[netperf](https://github.com/HewlettPackard/netperf) - measure network performance, test unidirectional throughput, and end-to-end latency.
[netpipe](https://linux.die.net/man/1/netpipe) - network protocol independent performance evaluator.
[nfsometer](http://wiki.linux-nfs.org/wiki/index.php/NFSometer) - NFS performance framework.
[nuttcp](https://www.nuttcp.net/Welcome%20Page.html) - measure network performance.
[phoronix-test-suite](https://www.phoronix-test-suite.com/) - comprehensive automated testing and benchmarking platform.
[seeker](https://github.com/fidlej/seeker) - portable disk seek benchmark.
[siege](https://github.com/JoeDog/siege) - http load tester and benchmark.
[sockperf](https://github.com/Mellanox/sockperf) - network benchmarking utility over socket API.
[spew](https://linux.die.net/man/1/spew) - measures I/O performance and/or generates I/O load.
[stress](https://people.seas.harvard.edu/~apw/stress/) - workload generator for POSIX systems.
[sysbench](https://github.com/akopytov/sysbench) - scriptable database and system performance benchmark.
[tiobench](https://github.com/mkuoppal/tiobench) - threaded IO benchmark.
[unixbench](https://github.com/kdlucas/byte-unixbench) - the original BYTE UNIX benchmark suite, provide a basic indicator of the performance of a Unix-like system.
[wrk](https://github.com/wg/wrk) - HTTP benchmark.
2018-04-27 08:09:36 +00:00
## Hardware
2018-04-12 06:15:22 +00:00
[[back to top](#handy-bash-oneliner-commands)]
##### Finding Out memory device detail
```bash
sudo dmidecode -t memory
2018-01-02 02:17:50 +00:00
```
2017-09-28 05:28:23 +00:00
##### Print detail of CPU hardware
```bash
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
2018-01-17 05:36:56 +00:00
```bash
lsscsi|grep SEAGATE|wc -l
or
sg_map -i -x|grep SEAGATE|wc -l
2018-01-17 05:36:56 +00:00
```
2018-05-31 02:55:20 +00:00
##### Get UUID of a disk (e.g. sdb)
```bash
blkid /dev/sdb
```
##### Print detail of all hard disks
2016-07-01 10:52:19 +00:00
```bash
lsblk -io KNAME,TYPE,MODEL,VENDOR,SIZE,ROTA
#where ROTA means rotational device / spinning hard disks (1 if true, 0 if false)
```
2018-02-12 06:56:35 +00:00
##### List information about NIC
```bash
lsscsi|grep -i 'ethernet'
```
2018-02-12 06:56:35 +00:00
##### Found out power status of the server
```bash
ipmitool -U your_bmc_username -P your_bmc_userpassword -I lanplus -H your_bmc_ip_address power status
```
2018-02-12 06:56:35 +00:00
##### Found out server sensor temperature
```bash
ipmitool sensors |grep -i Temp
2016-07-01 10:52:19 +00:00
```
## Others
2018-04-12 06:15:22 +00:00
[[back to top](#handy-bash-oneliner-commands)]
##### Remove newline / nextline
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
tr --delete '\n' <input.txt >output.txt
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Replace newline
2016-07-01 10:52:19 +00:00
```bash
tr '\n' ' ' <filename
2016-07-01 10:52:19 +00:00
```
2016-06-14 06:57:38 +00:00
##### To uppercase/lowercase
2016-07-01 10:52:19 +00:00
```bash
tr /a-z/ /A-Z/
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Compare files (e.g. fileA, fileB)
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
diff fileA fileB
# a: added; d:delete; c:changed
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
or
2016-07-01 10:52:19 +00:00
```bash
sdiff fileA fileB
# side-to-side merge of file differences
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Number a file (e.g. fileA)
2016-07-01 10:52:19 +00:00
```bash
nl fileA
2016-07-01 10:52:19 +00:00
```
or
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
nl -nrz fileA
# add leading zeros
2016-07-01 10:52:19 +00:00
```
or
```bash
nl -w1 -s ' '
# making it simple, blank seperated
```
##### Combine/ paste two files (e.g. fileA, fileB)
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
paste fileA fileB
# default tab seperated
2016-07-01 10:52:19 +00:00
```
##### Reverse string
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo 12345| rev
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Read .gz file without extracting
2016-07-01 10:52:19 +00:00
```bash
zmore filename
2016-07-01 10:52:19 +00:00
```
or
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
zless filename
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Run in background, output error file
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
some_commands &>log &
2016-07-01 10:52:19 +00:00
```
or
2016-07-01 10:52:19 +00:00
```bash
some_commands 2>log &
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
or
2016-07-01 10:52:19 +00:00
```bash
some_commands 2>&1| tee logfile
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
or
2016-07-01 10:52:19 +00:00
```bash
some_commands 2>&1 >>outfile
#0: standard input; 1: standard output; 2: standard error
2016-07-01 10:52:19 +00:00
```
##### Send mail
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
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")
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### .xls to csv
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
xls2csv filename
2016-07-01 10:52:19 +00:00
```
##### Append to file (e.g. hihi)
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo 'hihi' >>filename
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Make BEEP sound
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
speaker-test -t sine -f 1000 -l1
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Set beep duration
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
(speaker-test -t sine -f 1000) & pid=$!;sleep 0.1s;kill -9 $pid
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### History edit/ delete
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
~/.bash_history
2016-07-01 10:52:19 +00:00
```
or
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
history -d [line_number]
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Get last history/record filename
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
head !$
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Clean screen
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
clear
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
or
2016-07-01 10:52:19 +00:00
```bash
Ctrl+l
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Send data to last edited file
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
cat /directory/to/file
echo 100>!$
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Run history number (e.g. 53)
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
!53
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Run last command
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
!!
2016-07-01 10:52:19 +00:00
```
##### Run last command that began with (e.g. cat filename)
2016-07-01 10:52:19 +00:00
```bash
!cat
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
or
2016-07-01 10:52:19 +00:00
```bash
!c
# run cat filename again
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Extract .xf
1.unxz filename.tar.xz
2.tar -xf filename.tar
##### Install python package
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
pip install packagename
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Delete current bash command
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
Ctrl+U
2016-07-01 10:52:19 +00:00
```
2016-07-01 10:52:19 +00:00
or
2016-07-01 10:52:19 +00:00
```bash
Ctrl+C
2016-07-01 10:52:19 +00:00
```
or
2016-07-01 10:52:19 +00:00
```bash
Alt+Shift+#
# to make it to history
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Add something to history (e.g. "addmetohistory")
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
#addmetodistory
#just add a "#" before~~
2016-07-01 10:52:19 +00:00
```
2016-06-16 06:52:03 +00:00
##### Sleep awhile or wait for a moment or schedule a job
2016-06-16 06:52:03 +00:00
2016-07-01 10:52:19 +00:00
```bash
sleep 5;echo hi
2016-07-01 10:52:19 +00:00
```
2016-06-14 06:57:38 +00:00
##### Backup with rsync
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
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
2016-07-01 10:52:19 +00:00
```
//skip files that are newer on receiver (i prefer this one!)
##### Make all directories at one time!
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```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
2016-07-01 10:52:19 +00:00
```
##### Run command only if another command returns zero exit status (well done)
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
cd tmp/ && tar xvf ~/a.tar
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Run command only if another command returns non-zero exit status (not finish)
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
cd tmp/a/b/c ||mkdir -p tmp/a/b/c
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Extract to a path
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
tar xvf -C /path/to/directory filename.gz
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Use backslash "\" to break long command
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
cd tmp/a/b/c \
> || \
>mkdir -p tmp/a/b/c
2016-07-01 10:52:19 +00:00
```
##### Get pwd
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
VAR=$PWD; cd ~; tar xvf -C $VAR file.tar
# PWD need to be capital letter
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### List file type of file (e.g. /tmp/)
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
file /tmp/
# tmp/: directory
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Bash script
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
#!/bin/bash
file=${1#*.}
# remove string before a "."
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
file=${1%.*}
# remove string after a "."
2016-07-01 10:52:19 +00:00
```
##### Search from history
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
Ctrl+r
2016-07-01 10:52:19 +00:00
```
##### Python simple HTTP Server
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
python -m SimpleHTTPServer
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Read user input
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
read input
echo $input
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Generate sequence 1-10
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
seq 10
2016-07-01 10:52:19 +00:00
```
##### Find average of input list/file
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
i=`wc -l filename|cut -d ' ' -f1`; cat filename| echo "scale=2;(`paste -sd+`)/"$i|bc
2016-07-01 10:52:19 +00:00
```
2016-06-17 10:55:54 +00:00
##### Generate all combination (e.g. 1,2)
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
echo {1,2}{1,2}
# 1 1, 1 2, 2 1, 2 2
2016-07-01 10:52:19 +00:00
```
##### Generate all combination (e.g. A,T,C,G)
2016-06-17 10:55:54 +00:00
2016-07-01 10:52:19 +00:00
```bash
set = {A,T,C,G}
group= 5
for ((i=0; i<$group; i++));do
repetition=$set$repetition;done
bash -c "echo "$repetition""
2016-07-01 10:52:19 +00:00
```
2016-06-14 06:57:38 +00:00
##### Read file content to variable
2016-09-01 09:24:27 +00:00
```bash
foo=$(<test1)
2016-09-01 09:24:27 +00:00
```
2016-06-14 06:57:38 +00:00
##### Echo size of variable
2016-09-02 07:40:41 +00:00
```bash
echo ${#foo}
2016-09-02 07:40:41 +00:00
```
##### Echo tab
2016-09-02 07:40:41 +00:00
2016-09-10 09:39:01 +00:00
```bash
echo -e ' \t '
2016-09-10 09:39:01 +00:00
```
2016-09-02 07:40:41 +00:00
##### Array
2016-09-10 09:46:30 +00:00
```bash
declare -A array=()
2016-09-10 09:46:30 +00:00
```
##### Send a directory
2017-01-06 04:32:31 +00:00
```bash
scp -r directoryname user@ip:/path/to/send
2017-01-06 04:32:31 +00:00
```
2016-09-10 09:46:30 +00:00
##### Split file into lines (e.g. 1000 lines/smallfile)
2017-01-06 04:37:00 +00:00
```bash
$ split -d -l 1000 bigfilename
2017-01-06 04:37:00 +00:00
```
##### Create a large amount of dummy files (e.g 100000 files, 10 bytes each):
2017-01-06 08:16:43 +00:00
```bash
#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
2017-01-06 08:16:43 +00:00
```
##### Rename all files (e.g. remove ABC from all .gz files)
```bash
rename 's/ABC//' *.gz
```
2018-05-25 09:19:22 +00:00
##### Remove file extension (e.g remove .gz from filename.gz)
```bash
basename filename.gz .gz
2017-01-23 10:18:38 +00:00
zcat filename.gz> $(basename filename.gz .gz).unpacked
```
##### Add file extension to all file(e.g add .txt)
```bash
rename s/$/.txt/ *
# You can use rename -n s/$/.txt/ * to check the result first, it will only print sth like this:
# rename(a, a.txt)
# rename(b, b.txt)
# rename(c, c.txt)
```
##### Use the squeeze repeat option (e.g. /t/t --> /t)
2017-01-23 10:19:41 +00:00
```bash
tr -s "/t" < filename
2017-01-23 10:19:41 +00:00
```
##### Do not print nextline with echo
```bash
echo -e 'text here \c'
```
##### Use the last argument
```bash
!$
```
2017-01-06 08:16:43 +00:00
##### Check last exit code
```bash
echo $?
```
##### View first 50 characters of file
```bash
head -c 50 file
```
##### Group/combine rows into one row
```bash
2018-04-10 02:15:04 +00:00
#e.g.
#AAAA
#BBBB
#CCCC
#DDDD
cat filename|paste - -
-->
AAAABBBB
CCCCDDDD
cat filename|paste - - - -
-->
AAAABBBBCCCCDDDD
```
##### Fastq to fasta
2017-06-30 09:26:26 +00:00
```bash
cat file.fastq | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' >file.fa
2017-06-30 09:26:26 +00:00
```
##### Cut and get last column
2017-08-23 00:53:20 +00:00
```bash
cat file|rev | cut -d/ -f1 | rev
2017-08-23 00:53:20 +00:00
```
##### Add one to variable/increment/ i++ a numeric variable (e.g. $var)
2017-08-28 01:51:29 +00:00
```bash
((var++))
or
var=$((var+1))
2017-08-28 01:51:29 +00:00
```
2017-08-23 00:53:20 +00:00
##### 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.
2017-08-28 02:58:22 +00:00
##### Clear the contents of a file (e.g. filename)
2017-08-23 09:17:47 +00:00
```bash
>filename
2017-08-23 09:17:47 +00:00
```
##### Unzip tar.bz2 file (e.g. file.tar.bz2)
2017-08-23 09:17:47 +00:00
```bash
tar xvfj file.tar.bz2
2017-08-23 09:17:47 +00:00
```
##### Unzip tar.xz file (e.g. file.tar.xz)
```bash
unxz file.tar.xz
tar xopf file.tar
```
##### Output a y/n repeatedly until killed
'y':
2017-09-20 07:33:16 +00:00
```bash
yes
2017-09-20 07:33:16 +00:00
```
or 'n':
2017-10-06 07:48:47 +00:00
```bash
yes n
2017-10-06 07:48:47 +00:00
```
or 'anything':
2017-10-06 07:48:47 +00:00
```bash
yes anything
2017-10-06 07:48:47 +00:00
```
For example:
2017-10-06 07:48:47 +00:00
```bash
yes | rm -r large_directory
```
##### Create dummy file of certain size instantly (e.g. 200mb)
2018-02-07 10:23:31 +00:00
```bash
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
```
2017-10-06 07:48:47 +00:00
Standard output:
200+0 records in
200+0 records out
209715200 bytes (210 MB) copied, 0.0955679 s, 2.2 GB/s
2017-09-01 02:46:34 +00:00
##### Cat to a file
```bash
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)
```bash
watch -n 1 wc -l filename
```
2017-09-20 07:33:16 +00:00
##### Print commands and their arguments when execute (e.g. echo `expr 10 + 20 `)
2017-10-19 05:38:40 +00:00
```bash
set -x; echo `expr 10 + 20 `
```
##### Print some meaningful sentences to you (install fortune first)
```bash
fortune
```
##### Colorful (and useful) version of top (install htop first)
```bash
htop
```
##### Press any key to continue
```bash
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:
2017-10-31 02:15:07 +00:00
```bash
q -d "," "select c3,c4,c5 from /path/to/file.txt where c3='foo' and c5='boo'"
```
##### Sreen and tmux
create session and attach:
2017-10-31 02:15:07 +00:00
```bash
screen
or
tmux
```
create detached session foo:
```bash
screen -S foo -d -m
or
tmux new -s foo -d
```
detached session foo:
```bash
screen: ^a^d
or
tmux: ^bd
```
2017-09-20 07:33:16 +00:00
list sessions:
```bash
screen -ls
or
tmux ls
```
attach:
```bash
screen -r
or
tmux attach
```
attach to session foo:
```bash
screen -r foo
or
tmux attach -t foo
```
kill session foo:
```bash
screen -r foo -X quit
or
tmux kill-session -t foo
```
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scroll:
(screeen)
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Hit your screen prefix combination (C-a / control+A), then hit Escape.
Move up/down with the arrow keys (↑ and ↓).
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Redirect output of an already running process in screen:
(C-a / control+A), then hit 'H'
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store screen output for screen:
Ctrl+A, Shift+H
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You will then find a screen.log file under current directory.
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(tmux)
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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:
```bash
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Ctrl-B
:setw synchronize-panes
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# 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
```
##### Cut the last column
```bash
cat filename|rev|cut -f1|rev
```
##### pass password to ssh
```bash
sshpass -p mypassword ssh root@10.102.14.88 "df -h"
```
##### wait for a pid (job) to complete
```bash
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
```bash
sudo apt-get install poppler-utils
pdftotext example.pdf example.txt
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```
##### list only directory
```bash
ls -ld -- */
```
##### Capture/record/save terminal output (capture everything you type and output)
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```bash
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.
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```bash
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
#
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```
##### set up virtualenv(sandbox) for python
```bash
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#1. install virtualenv.
sudo apt-get install virtualenv
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#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
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#4. you can check check if you are now inside a sandbox.
type pip
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#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
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```
##### working with json data
```bash
#install the useful jq package
#sudo apt-get install jq
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#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'
```
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##### Editing your history
```bash
history -w
vi ~/.bash_history
history -r
```
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##### Decimal to Binary (e.g get binary of 5)
```bash
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)
```bash
echo "00110010101110001101" | fold -w4
#0011
#0010
#1011
#1000
#1101
```
##### sort a file by column and keep the original order
```bash
sort -k3,3 -s
```
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##### Right align a column (right align the 2nd column)
```bash
cat file.txt|rev|column -t|rev
```
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=-=-=-=-=-A lot more coming!! =-=-=-=-=-=-=-=-=-=waitwait-=-=-=-=-=-=-=-=-=-