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Navigating the Server: Bash Commands

Notes by: Pagé Goddard

Tutorial session by: Jennifer Liberto

Contents

look at your directory contents

  • ls lists just the file and subfolder names in your directory
  • ls -1 does the same, but puts it all in a single column
  • ll lists contents with permissions, size, and date information
  • ls -lrta list in reverse time, anything (lists latest last in list)

permissions

drwxr-xr-- example 1 -rwxr-xr-- example 2

  • initial d = directory; - = file
  • w = can write
  • x = can execute
  • r = can read

changing directories

pwd
/media/burchardraid01/datafreeze # example directory

cd .. && pwd # change then prnt new directory
/media/burchardraid01 # parent directory

cd ~ && pwd
/media/.../your.directory # you are now in your home directory

cd path/to/desired/directory && pwd
path/to/desired/directory # you are now in the directory you asked for

pwd = print working directory; tells you where you are

cd = change directory

. = current directory

.. = previous directory

~ = home

note: when typing a path, use / not backslash; if you get an error, check that you are not trying to cd into a file instead of the directory; if error persists, check your slashes, your capitalization and your path

visualize files

less filename = opens 1 page view of data without printing the whole thing to screen; move by line (arrow keys) or page (space)

head filename = prints first 10 lines of file

  • head -3 filename = prints first 3 lines
  • tail filename = prints last 10 lines of file
  • tail -3 filename = print last 3 lines
  • head 10 filenme | tail -3 - = print 3 lines after line 10 of file
  • cut -d' ' -f 1-5 filename = print columns 1-5 of file; d is your file delimiter (the symbol that separates columns, usually space ' ', comma ',', or tab '\t')
  • cut -d' ' -f 1-5 filename | head -5 - = print only rows 1-5 of columns 1-5 of file

vim filename = let's you view and edit file

  • to edit, press i (for insert) and write as you please
  • navigate lines with arrow keys
  • to save click Esc and type :w
  • to quit, click Esc and type :q
  • to save and quit type :wq

run a process in the background

this is especially useful if you are running an automated script that will take a while and doesn't require interaction after it starts

start a new screen

screen 
# this changes your console window to a detachable "screen"
# title will now read "screen 0: username@hostname:~/PATH/TO/current_directory"
# normal title bar reads: "username@hostname:~/PATH/TO/current_directory"

start a new screen with a particular name

screen -S name

detach your screen

# while in the new screen  type
ctrl+A ctrl+D

return to your screen

screen -r  # if you only have one screen
# if you have multiple screens, the list will print here

screen -r [number/name] # if returning to one of multiple screens

kill an old screen

screen -r [name/number] # return to screen

# type
crtl+A K

copying files to your computer

on a mac/linux
exit # leave server
scp username@hostname.edu:path/to/file/filename.csv ~/Desktop
  • translation: copy/paste [this file on server] [to my personal desktop]
  • scp = secure copy paste (copy paste over secure ssh connection)
  • to push to server, just switch ~/Desktop and username@hostname.edu:/path
or use filezilla GUI

Angel's step-by-step instructions for setting up FileZilla can be found on the Wiki here

Congrats! you can now read your data into R studio from your personal computer