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====== 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/''