I often find myself looking for some shortcuts for working on the terminal with bioinformatics data, so here is a list of the most useful shortcuts and commands for the Unix terminal (credits to cheatsheetworld):


File system

ls  –  list items in the current directory
ls -l  –  list items in the current directory in a long format, to see permissions, size and modification date
ls -a  –  list all items in the current directory, including hidden files
ls -F  –  list items in the current directory showing directories with a slash and executables with a star
ls [dir]  –  list items in the directory [dir]
cd [dir]  –  change directory to [dir]
cd ..  –  go up one directory
cd /  –  go to the root directory
cd ~  –  go to current user’s home directory
cd -  –  go back to the last directory you were in
pwd  –  show the current working directory
mkdir [dir]  –  create a new directory [dir]
rm [file]  –  remove the file [file]
rm -r [dir]  –  remove the directory [dir] recursively
cp [file1] [file2]  –  copy [file1] to [file2]
cp -r [dir1] [dir2]  –  copy directory [dir1] to [dir2] recursively
mv [file1] [file2]  –  move or rename [file1] to [file2]
ln -s [file] [link]  –  create a symbolic link to [file]
touch [file]  –  create [file]
cat [file]  –  output the content of [file] to the stdout device (terminal screen)
less [file]  –  view the content of [file] with page navigation
head [file]  –  output the first 10 lines of [file]
head -n [num] [file]  –  output the first [num] lines of [file]
tail [file]  –  output the last 10 lines of [file]
tail -n [num] [file]  –  output the last [num] lines of [file]
vim [file]  –  edit [file] in the terminal
alias [name] '[command]'  –  create an alias named [name] for the [command] command


Compression

tar cf [file.tar] [files]  –  create a tar-compressed archive named [file.tar] containing [files]
tar czf [file.tar.gz] [files]  –  create a tar-compressed archive using Gzip compression named [file.tar] containing [files]
tar xf [file.tar]  –  extract the files contained in [file.tar]
tar xzf [file.tar]  –  extract the files contained in [file.tar] using Gzip
gzip [file]  –  compress [file] and rename the archive to [file].gz
gzip -d [file.gz]  –  extract the files contained in [file.gz]


System

shutdown  –  shut down the machine
reboot  –  restart the machine
date  –  show the current date and time
whoami  –  show who is currently logged in
finger [user]  –  display information about [user]
man [command]  –  show the manual for [command]
df  –  show disk usage
du  –  show directory space usage
free  –  show memory and swap usage
whereis [app]  –  search for possible locations of [app]
which [app]  –  show the path of [app] that will be run by default


Networking

wget [url]  –  download a file hosted at [url] (mostly on Linux os)
curl [url]  –  download a file hosted at [url] (mostly on Mac os)
scp [user]@[host]:[file] [dir]  –  secure-copy [file] from the [host] remote server to the [dir] directory on the local machine
scp [file] [user]@[host]:[dir]  –  secure-copy [file] from the local machine to the [dir] directory on the [host] remote server
ssh -p [port] [user]@[host]  –  connect to the [host] remote server as user [user] using port [port]
ping [host]  –  ping [host] and output results
whois [domain]  –  get information for [domain]
dig [domain]  –  get DNS information for [domain]


Shortcuts

ctrl + a  –  move cursor to the beginning of line
ctrl + f  –  move cursor to the end of line
alt + f  –  move cursor forward 1 word
alt + b  –  move cursor backward 1 word


Process Management

ps  –  display your currently active processes
top  –  display all running processes
kill [pid]  –  kill the process with id [pid]
kill -9 [pid]  –  force-kill the process with id [pid]


Permissions

chmod [ugo] [file]  –  change permissions of [file] to [ugo]: [u] represents the user’s permissions, [g] represents the user group’s permissions, [o] represents everyone else’s permissions. The values of [u], [g] and [o] can be any number between 0 and 7
7  –  full permissions
6  –  read and write only
5  –  read and execute only
4  –  read only
3  –  write and execute only
2  –  write only
1  –  execute only
0  –  no permissions
chmod 600 [file]  –  current user can read and write [file]
chmod 700 [file]  –  current user can read, write and execute [file]
chmod 755 [file]  –  current user can read, write and execute [file], while everyone else can only read and execute


Searching

grep [pattern] [file]  –  search for [pattern] in [file]
grep -r [pattern] [dir]  –  search recursively for [pattern] in [dir]
grep -rn [pattern] [dir]  –  search recursively for [pattern] in [dir] and show the line number found
[command] | grep [pattern]  –  search for [pattern] in the output of [command]
find [file]  –  find all instances of [file]
locate [file]  –  find all instances of [file] using an indexed database built from the updatedb command (faster than find)
sed -i 's/[day]/[night]/g' [file]  –  find all occurrences of [day] in [file] and replace them with [night]; s represents substitution and g means global
 

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