The purpose of this cheat sheet is to introduce biologist and bioinformatician to the frequently used tools for NGS analysis as well as giving experience in writing one-liners.
File System ls — list items in current directory ls -l — list items in current directory and show in long format to see perimissions, size, and modification date ls -a — list all items in current directory, including hidden files ls -F — list all items in current directory and show directories with a slash and executables with a star ls dir — list all items in directory dir cd dir — change directory to dir cd .. — go up one directory cd / — go to the root directory cd ~ — go to to your home directory cd - — go to the last directory you were just in pwd — show present working directory mkdir dir — make directory dir rm file — remove file rm -r dir — remove directory dir recursively cp file1 file2 — copy file1 to file2 cp -r dir1 dir2 — copy directory dir1 to dir2 recursively mv file1 file2 — move (rename) file1 to file2 ln -s file link — create symbolic link to file touch file — create or update file cat file — output the contents of file less file — view file with page navigation head file — output the first 10 lines of file tail file — output the last 10 lines of file tail -f file — output the contents of file as it grows, starting with the last 10 lines vim file — edit file alias name 'command' — create an alias for a command
System shutdown — shut down machine reboot — restart machine date — show the current date and time whoami — who you are logged in as 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 — show possible locations of app which app — show which app will be run by default
Process Management ps — display your currently active processes top — display all running processes kill pid — kill process id pid kill -9 pid — force kill process id pid
Permissions ls -l — list items in current directory and show permissions chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is 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 — you can read and write - good for files chmod 700 file — you can read, write, and execute - good for scripts chmod 644 file — you can read and write, and everyone else can only read - good for web pages chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
Networking wget file — download a file curl file — download a file scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine ssh user@host — connect to host as user ssh -p port user@host — connect to host on port as user ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login ping host — ping host and output results whois domain — get information for domain dig domain — get DNS information for domain dig -x host — reverse lookup host lsof -i tcp:1337 — list all processes running on port 1337
Searching grep pattern files — search for pattern in files 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 grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension command | grep pattern — search for pattern in the output of command find file — find all instances of file in real system locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
Compression tar cf file.tar files — create a tar named file.tar containing files tar xf file.tar — extract the files from file.tar tar czf file.tar.gz files — create a tar with Gzip compression tar xzf file.tar.gz — extract a tar using Gzip gzip file — compresses file and renames it to file.gz gzip -d file.gz — decompresses file.gz back to file
Shortcuts ctrl+a — move cursor to beginning of line ctrl+f — move cursor to end of line alt+f — move cursor forward 1 word alt+b — move cursor backward 1 word
