unix shell tutorial

navigating files & directories

• man <command> : opens manual for that command
• syntax of shell command:

• shortcuts
  • cd : go to home directory
  • ~ : home directory
• options for ls
  • -s : display size of files & directories
  • -S : sort files & directories by size
  • -F : classify output (* = executable, / = directory, @ = link)
  • -l : long list format (additional info)
  • -h : “human readable”
  • -a : show all (useful for hidden directories)
  • -R : list all nested subdirectories

working with files & directories

• mkdir options:

  • -p create directories with nested subdirectories

    $ mkdir -p ../project/data ../project/results

• create text file: vi <name>.txt

  • created in current directory

• create file: touch <name>.<extension>

  • empty file created in current directory

• move to a new folder:

  • *$ mv sucrose.dat maltose.dat ../raw (*moves both files to raw folder)
  • *$ mv *.dat analyzed (*moves all files ending in .dat to analyzed folder)

• cp options:

  • -r : copies directory & all its contents

• rm options:

  • -i : asks for confirmation to delete files
  • -r : remove a directory & all its contents

pipes & filters

• wc options:
  • -l : only show number of lines
  • -w : only show number of words
  • -m : only show number of characters
• less [file] : displays a screenful of file
  • next: spacebar
  • back: b
  • quit: q
• sort options:
  • -n : numerical sort
  • -r : reverse order
• head options:
  • -n [number] : display first [number] lines
• cut : cuts out certain sections of each line in file
  • -d : specify delimiter character
  • -f [number] : specify which field to extract

git commands

<aside> 💡 current directory must be a repository

</aside>

• git log : check history
• git help or man git -<verb> : get help (q to exit)
• git add [file] : add file to “staging area”
• git commit -m “comment” : commit to the repository
• git push -u origin main : push changes from local to remote repository (in “main” branch)
• git status : check status
• git diff : check difference
• git pull : pull changes from remote to local repository
• git branch: lists branches
• git branch [name]: creates new branch
• git checkout [branch]: switch to branch
• git merge [branch]: merges changes from listed branch to current branch

other

vi commands

• [esc] : enter command mode
• in command mode:
  • :wq exit vi (& save changes)