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Bacterial WGS training : Exercise 1

Title Linux command line.
Training dataset: None
Questions:
  • How do I use the command line?
  • How do I navigate the file system?
Objectives:
  • Learn/Remember how to use the command line.
  • Learn/Remember how to navigate through the Linux file system.
Time estimation: 30 min
Key points:
  • Remeber the shell basic commands: pwd cd ls mkdir rmdir mv nano cat less more head tail rm

‼️ Important things to remnenber:

  • Use Tab to automatically complete file names and paths, so it can be easiert to write in the terminal
  • Use keyboard arrows (:arrow_up: :arrow_down:) to move through your terminal's history, so you don't have to write the commands again.
  • Try not to use spaces, accents or special characters like "Ñ" letter, when writting directory of file names.
  • Basic commands you should always remember: pwd cd ls mkdir mv rm rmdir less nano

Answering to main questions

How do I use the command line?

Open a terminal by clicking in the icon or typing Ctrl+Alt+T. Now you can type in the prompt.

How do I navigate the file system?

Let's remember the basics: pwd cd ls mkdir mv rm rmdir less nano. We are going to use those commands to:

Checking the working directory (pwd)

Check our working directory:

pwd
#Output: /home/alumno

Moving between directories (cd)

Move to our Desktop folder:

cd ~/Escritorio
pwd
#Output: /home/alumno/Escritorio

Move to the course folder:

cd 
pwd
#Output: /home/alumno
cd wgs
pwd
#Output: /home/alumno/wgs
cd bacterial_wgs_training_dataset/RAW/FULL_DATA
pwd
#Output: /home/alumno/wgs/bacterial_wgs_training_dataset/RAW/FULL_DATA
cd .
pwd
#Output: /home/alumno/wgs/bacterial_wgs_training_dataset/RAW/FULL_DATA
cd ..
pwd
#Output: /home/alumno/wgs/bacterial_wgs_training_dataset/RAW/
cd ../../..
pwd
#Output: /home/alumno/

Questions:

Which is the meaning of the "~" symbol?

It is the abreviation of /home/user/ path

What does de `cd` command without arguments do?

It changes the current directory to /home/user/ path.

What does "." mean? Current directory
What does ".." mean? Parent directory

Listing directories (ls)

cd wgs
cd bacterial_wgs_training_dataset
ls
#Output: ANALYSIS RAW  REFERENCES  RESULTS

This is the folder structure we will use for this training. Now we are going to list the files in the REFERENCE folder:

ls REFERENCES

This command will output a big list of files, which are the files that we will usea as REFERENCE through the different exercises of the training. Now wi will run this other command:

ls /home/alumno/wgs/bacterial_wgs_training_dataset/REFERENCES/

Questions:

What does ".." mean? Parent directory
Which is the difference between this last command and the previous one? There is no difference, they are listing the content of the exact same directory.
Do they display the same information? Yes!
Which one is relative path?

ls REFERENCES

Which one is absolute path?

ls /home/alumno/wgs/bacterial_wgs_training_dataset/REFERENCES/

Let's see different parameters for the ls command. Write:

ls REFERENCES
ls -l REFERENCES
ls -a REFERENCES
ls -la REFERENCES

Questions:

What does de different arguments of ls do?
-l : Long listing format: Displays the permission information

-a : All files: Lists also hiddent files

-la : Long format listing and hidden files together.
What does the new file special? It is a hidden file, whose file name starts by dot.

⚠️ REMINDER: ⚠️ EVERY TIME YOU CHANGE DIRECTORY (cd) YOU HAVE TO CHECK YOUR PATH (pwd) AND LIST THE FILES INSIDE (ls) TO CHECK YOU DIDN'T MAKE MISTAKES

Creating and removing directories (mkdir & rmdir)

Now we are going to move to the ANALYSIS folder which is the folder were we will run all the exercises

cd ANALYSIS
pwd
#Output: /home/alumno/wgs/bacterial_wgs_training_dataset/ANALYSIS
ls

As you can see the folder is empty, so now we will fill this folder. Create a directory for this handson: Remember: Linux is case sensitive and does not like white spaces in names

mkdir 01-handsonLinux
ls
#Output: 01-handsonLinux

Now type:

mkdir 01-handsonlinux 01-HandsOnLinux
ls
#Output: 01-handsonlinux 01-handsonLinux 01-HandsOnLinux

Questions:

Is it possible to create more than one directory at the same time? Yes, it is!
If the names of the folders are the same, why it creates three different directories? Because it is case sensitive, so the names are not exactly the same!

Now we will remove the extra directories:

rmdir 01-handsonLinux 01-HandsOnLinux
ls
#Output: 01-handsonlinux
Moving and renaming files (mv)

Move to the new folder

cd 01-handsonlinux
pwd
#Output: /home/alumno/wgs/bacterial_wgs_training_dataset/ANALYSIS/01-handsonlinux

We are going to move the hidden file in REFERENCE folder to this directory and then rename it:

mv ../../REFERENCES/.ThisIsAHiddenFile .
ls
ls -a
mv .ThisIsAHiddenFile NowImNotHidden
ls -a
ls

Questions:

Which is the difference between the two `mv` commands? The first one moves a file to a different folder and the second one renames the file.
Do you remember what "." mean from the first questions? Current directory
And ".."? Parent directory

⚠️ REMINDER: ⚠️ LINUX DOES NOT REQUIRE FILE EXTENSIONS

Editing files and displaying them (nano & cat)

We are going to read the file and edit it:

cat NowImNotHidden
#Output: I'm a hidden file.

This is not true, so we are going to edit it:

nano NowImNotHidden

Write: I'm not a hidden file.

And save it: Ctrl + O + Intro

Close the new file: Ctrl + X

Now read the new file:

cat NowImNotHidden
#Output: I'm not a hidden file.
ls
#Output: NowImNotHidden
cd ../../
Read files other ways (less & more & head & tail)

And now we will read this file:

cat REFERENCES/bacterial_wgs_training_initial.tree
less REFERENCES/bacterial_wgs_training_initial.tree

⚠️ Remember: To close less press "q"

more REFERENCES/bacterial_wgs_training_initial.tree

⚠️ Remember: To close more press "q"

head REFERENCES/bacterial_wgs_training_initial.tree
tail REFERENCES/bacterial_wgs_training_initial.tree
head -n4 REFERENCES/bacterial_wgs_training_initial.tree
tail -n3 REFERENCES/bacterial_wgs_training_initial.tree

Questions:

Which is the difference between head and tail?
Head displays first lines of a file.

Tail displays the last lines of a file

What does the argument -nX do to tail and head?

 Displays de X numbers of lines from the begining (head) or end (tail) of a file.
Removing a file (rm)

Now we will learn how to remove files:

cd ANALYSIS/01-handsonlinux/
pwd
ls
#Output: NowImNotHidden
mv ../../REFERENCES/bacterial_wgs_training_initial.tree .
ls
#Output: bacterial_wgs_training_initial.tree NowImNotHidden
rm NowImNotHidden
ls
#Output: bacterial_wgs_training_initial.tree