Linux Essential Commands

man: manual page.
- Explains how to use a shell command.
- man <COMMAND>: For example, to find out how to use man, type man man
ls: list directory content
cd: change directory
pwd: print working directory
wc: count word, line, character, and byte
head: display the first part of a file
- default = 10 lines, change by -n
- example: head -n 20 filename (display the first 20 lines of filename)
tail: display the last part of a file
cat: concatenate and print the file
more: display output one screen at a time
cp: copy file
- cp <SOURCE> <DESTINATION>
mv: move file (can be use as changing file name)
- mv <SOURCE> <DESTINATION>
rm: remove file (like delete)
- rm -r: remove directory (like rmdir)
chmod: change file modes or Access Control Lists
- (u,g,o): user, group, other
- (r,w,x): read, write, execute
chown: change file owner or group
mkdir: make directories
rmdir: remove directories
find: search for files
- examples:
  - find /PATH -type f -name “*.bam”: find all files (-type f) in /PATH with the name *.bam.
  - find /PATH -type d -name “flash”: find all directories (-type d) in /PATH with the name flash.
  - These examples are useful for calculating file sizes or clean up.
  - To calculate all file sizes, pipe the file names to xargs and du; find /PATH -type f -name “*.bam” | xargs du -csh
  - To remove all files found by the command, pipe the file names to xargs and rm; find ./ -type f -name “*.bam” | xargs rm
  - To remove all directories found by the command, pipe the directory names to xargs and rm -r; find ./ -type d -name “bwa_*” | xargs rm -r
ssh: OpenSSH SSH client (remote login program)
- ssh usrname@ip_adress
scp: secure copy (remote file copy program)
- scp <SOURCE> USRNAME@IP:<DESTINATION>
- scp USRNAME@IP:<SOURCE> <DESTINATION>
- -p: 保留原始檔案權限＆修改日期等, -r: 複製整個資料夾
2>&1: send STDERR to STDOUT (0:STDIN, 1:STDOUT, 2:STDERR)
&: running job in background (終端機背景執行)
- example: <COMMAND> &
- the job may be terminated if you log out
nohup: run a command in background; immune to hangups 系統背景執行
- nohup <COMMAND> &
- This is different from <COMMAND> &; logging out would not affect the job
kill: kill job
- kill PID: kill a job by the process id (PID)
- ps -u USER | grep blast | cut -d ' ' -f 2 | xargs kill: generate a list of all processes by USER, use grep to find blast jobs, cut out the PID, send to xargs to kill the jobs.
free: display amount of free and used memory in the system
- free -g: Display the amount of memory in gibibytes
grep: find keywords in file
- grep <KEYWORD> <FILENAME>
nice and renice: run a program with modified priority. If the server is under heavy load and you need to start a non-urgent large job, please use these.'
diff:
wget: download files
- example: download all '*gz' files in the link; use the '-e' command to force ignore the robot file (use with care)
  - wget -r –no-parent -e robots=off -A '*.gz' https://www.example.com/files/