Basic toolkit



  • Let’s dig into the most important BASH commands

  • We’ll do a type-along session

We will cover these commands

Read files and change file properties

  1. cat  print content on screen

  2. head  print first part

  3. tail  print last part

  4. less  browse content

  5. tar  compress or extract file

  6. chmod  change file permissions

  7. man  info about a command

File system Navigation

pwd — where are you now? “Print name of current/Working Directory”

$ pwd

$ pwd -P 
  • -P gives you the physical path,

    • ignores how you got there

ls — list directory contents

Type ls to display the contents of the current directory.

$ ls -a

-a also shows hidden files and directories.

$ ls -l

-l gives you listed and detailed information.

$ ls -lt

-lt sorts things by time modified.

$ ls –lrt

-r gives reversed order, so in this case newest in last line.

$ man ls
  • for complete information about a command.

  • TIP: -$ man <command> works for almost any command!

    • scroll with arrows and quit with q.

cd — Change the shell working Directory

  • To change directory, use cd <target>

$ cd /proj/introtouppmax

$ pwd

$ ls

$ cd labs

$ pwd

Experiment with cd

  • Experiment with cd.

  • Try adding <spaces> or extra / in various places.

  • Use tab completion to avoid typos and typing ls a lot.

  • Figure out the use of the following:

$ cd -

$ cd ..

$ cd

$ cd ~

Copy, Create, Move

mkdir — make directories


  • Make sure you’re in your home directory by cd ~

  • Create a new directory uppmax-intro

$ cd ~
$ mkdir uppmax-intro
  • Go in there:

 $ cd uppmax-intro/

cp — copy files and directories

  • Copy files with: cp <source> <target>

  • Set target to . to keep name and to point at present directory.

$ cp /proj/introtouppmax/labs/linux_tutorial/ .
  • Well, that didn’t work. What does the error say?

  • So… try

$ cp -r /proj/introtouppmax/labs/linux_tutorial/ .

-r is for recursive, meaning including files and subdirectories!

  • Move to your just created linux_tutorial/

$ cd linux_tutorial
  • Make a copy of the file “newfile” in the same directory:

$ cp newfile copyfile

scp —secure copy (remote file copy program)

  • Linux/MacOS: To copy data to/from Rackham, you can use scp from the terminal on your local machine:

  • Upload from present directory on local machine to your home directory on cluster.

    • Example (not done by us today)

[bob@macbook]$ scp myinput

[bob@macbook]$ scp myinput                      # (keeping filename)
  • Download

[bob@macbook]$ scp copyofmydata

[bob@macbook]$ scp .                      # (keeping file name)

mv — move/rename file

  • Moving files works just like copying files:

  • mv <source> <target>

  • Move the copy you just made to another place:

$ mv copyfile ../
  • Rename it.

$ mv ../copyfile ../renamedfile


tar — archiving and compression

  • We’re going to need more files. Let’s extract the tar.gz file (tared and gzipped file)

$ tar -vxzf files.tar.gz
  • The flags mean: - verbosely - extract - gzipped - filename

  • Order of flags may matter!

    • f should be in the start or in the end!

  • You should see a list of files being extracted


  • To compress use the flag -cinstead of -x

$ tar -czfv <tar file> <path/to/directory/file(s)-or-directory>


rm — delete files or directories


  • Tip: make “rm” ask if you really want to erase:

    • Within a session: Type in the command prompt

      alias rm='rm -i'
    • Override asking with

      rm –f <>
    • Edit file “.BASHrc” in /home directory by adding the alias line for this to start every time.

  • This will also work for mv and cp!

  • Deleting files works just like copying or moving them: rm <target>

  • Try it out:

$ rm ../renamedfile

$ rm this_is_empty
  • hmmmm…

rmdir — delete an empty directory

  • We need another command to delete directories

$ rmdir this_is_empty

$ rmdir this_has_a_file
  • Again??

  • Is there a way to use rm to delete directories?


man — manual, look up the right flags

  • Nobody can remember whether it’s -R or -r for recursive, or if -f lets you choose a file or forces an action.

$ man ls 
  • shows you how to use ls and all its options

  • Type /<keyword> to search for a keyword, use n (forward) and ´N` (backward) to scan through hits.

  • Scroll with arrows.

  • Type q to quit.


  • Spend some time now to browse the man pages for the commands you’ve just learned!

Let’s get wild with Wildcards


$ ls many_files

$ ls many_files/*.txt

$ ls many_files/file_1*1.docx
  • Want to clean out temporary files ending in .tmp in all the subdirectories?


  • NB! It could be wise to do ls -a */*.tmp first to see what will be deleted…

 $ rm */*.tmp


  • Exercise: Create a new directory and move all .txt files in many_files to it.

Reading files

  • In Linux, you can (if you wish) also display files without being able to change them

$ cd old_project

$ ls
  • Hmm, which of these files are useful?

cat - concatenate files and print on the standard output


  • cat dumps the contents of files to the terminal as text

 $ cat the_best
  • Yummy!

 $ cat a
  • What’s this???

  • Concatenate files with this wizardry:

 $ cat a the_best > combinedfiles.txt
  • File a is written first and the_best is appended

head — display the top (heading) of a file


 $ head a
  • You can choose how many lines to display (default 10)

 $ head -n 4 a

tail — display the end of a file


  • Tail is the same as head, but for the other end.

 $ tail -n 5 a
  • Handy to look at log files or to figure out the structure of a text file.

less — read a whole file

  • cat doesn’t really work for long files

 $ less a
  • Search with /<keyword> and n/N

  • Hit q to quit.

  • scroll with arrows.

  • man uses less!

    “less is more”

File permissions



$ ls -l

  drwxrwxr-x 2 marcusl marcusl 4096 Sep 19 2012 external_hdd 
  -rwxr-xr-x 1 marcusl marcusl 17198 Jul 16 14:12 files.tar.gz
  • Leading symbol:

    • d directory

    • - regular file

    • l symbolic link (more on this tomorrow)

    • Others exist, but you can ignore them for now

    $ ls -l
    drwxrwxr-x 2 marcusl marcusl 4096 Sep 19 2012 external_hdd
    -rwxr-xr-x 1 marcusl marcusl 17198 Jul 16 14:12 files.tar.gz
  • Three sets of “rwx” permissions

    • rwx: r ead, w rite, ex ecute

    • User: the user account that owns the file (usually the one that created it)

    • Group: the group that owns the file (usually the project group in /proj/xyz or the user’s group elsewhere)

    • Others: everyone else on the system (literally a thousand strangers)

  • r – read

    • Files: Read the contents of the file

    • Directories: List the files in the directory

  • w – write

    • Files: Modify the file

    • Directories: Add, rename, or delete files in the directory

  • x – execute

    • Files: Run the file as a program

    • Directories: Traverse the directory (e.g. with “cd”)

Changing permissions

chmod — change file mode bits

If you own, i.e. created, the file or directory, you can modify the content

Common issues

  • Files with w can be modified and destroyed by accident. Protect your data!

  • If you want to share data or scripts with a person not in your project (e.g. support staff like me), you can!

  • If you want to keep non-members from even seeing which files you have, you can!


chmod <mode> <files>

  • <mode> is of the form: For whom, Modify, What permission(s)

  • For whom?

    • u: user/owner

    • g: group, often the members to a certain project

    • o: others

    • a: all

    • if not set changes are applied for user AND group

  • Modify?

    • +: add permissions,

    • -: remove

    • =: set equal to

      • = usually causes unmentioned bits to be removed except that a directory’s unmentioned set user and group ID bits are not affected.

  • What permissions?

    • r, w, x, i.e. the actual permission


  • <mode> can be e.g.:

    • u+x : lets You (owner) run a script you just wrote

    • -w : no write permissions for owner+group

    • warning: if w was already set for others it will be kept!!

    • +rw : let user and group members read and edit this file, not others if not already set

    • =xw : let group members go into your directory and put files there, but not see which files are there, others are not affected

    • a=xw : set xw for everyone

  • chmod takes flags as usual, e.g.

    • -R for recursive (i.e. all files and sub-directories therein)

chmod — Hands-on

  • In your locally created linux_tutorial directory, find important files and old saved data that you wouldn’t want to lose (imagine).

    • Directories: important_results/, old_project/

    • File: last_years_data

  • Use chmod to remove write permission from those files and directories (use the -R flag (not -r) to also do the files in the directories).

    • Take a moment to play around with chmod and explore the effects of permissions on files and directories.

More about BASH command line and scripts on Tuesday and Wednesday!