2 Introduction to the command line

2.1 Set-up a terminal

MacOS/Linux: Launch terminal on your machine.

Windows users options: Windows Subsystem for Linux (WSL) –> It creates an Ubuntu terminal environment where you can code just like from a linux Ubuntu terminal. This is useful for the course as well as for practice working in bash. from ubuntu website and from the windows website

SSH client –> Windows: [MobaXterm]( https://mobaxterm.mobatek.net/download-home-edition.html . This is a very basic ssh client, meaning, it will allow you to connect to the server and it will serve as a terminal for the course.

If you are already using Visual Studio, it needs one ssh extension plugin to serve as a ssh.

Git for windows –> I am not sure this can be used as a ssh but, in regards to this course, it is also useful to practice coding on the terminal.

Very last-minute resource –> launch this terminal emulator in a new window.

2.2 Working with the command line

Most of the activities of the bioinformatic section of this workshop will be done using the Unix command line (Unix shell).
It is therefore highly recommended to have at least a basic grasp of how to get around in the Unix shell.
We will now dedicate one hour or so to follow some basic to learn (or refresh) the basics of the Unix shell.

[!question] What is the UNIX SHELL? What is Bash?

[!todo] The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as the terminal or command line. Some computers include a default Unix Shell program.

[!todo] The most popular Unix shell is Bash, Bash is a shell and a command language.

For a Mac computer running macOS Mojave or earlier releases, the default Unix Shell is Bash.

For a Mac computer running macOS Catalina or later releases, the default Unix Shell is Zsh. Your default shell is available via the Terminal program within your Utilities folder.

The default Unix Shell for Linux operating systems is usually Bash.

2.3 Playing around with basic UNIX commands

2.3.1 Some notes!

These commands:

mkdir unix_shell
cd unix_shell

…are commands you need to type in the shell. Each line is a command. Commands have to be typed in a single line, one at a time. After each command, hit “Enter” to execute it.

Things starting with a hashtag:

# This is a comment and is ignored by the shell

…are comments embedded in the code to give instructions to the user. Anything in a line starting with a # is ignored by the shell.

Different commands might expect different syntaxes and different types of arguments. Some times the order matters, some times it doesn’t! The best way to check how to run a command is by taking a look at its manual with the command man or to the –help for a shorter version of it:

man mkdir

# You can scroll down by hitting the space bar
# To quit, hit "q"

mkdir -h

# did it work?

2.3.2 Creating and navigating directories

First let’s see where we are:

pwd  # print working directory

Are there any files here? Let’s list the contents of the folder:

ls

# or 

ll

Let’s now create a new folder called unix_shell. In addition to the command (mkdir), we are now passing a term (also known as an argument) which, in this case, is the name of the folder we want to create:

mkdir unix_shell

Has anything changed? How to list the contents of the folder again?

HINT (CLICK TO EXPAND)

ls

And now let’s enter the unix_shell folder:

cd unix_shell

Did it work? Where are we now?

HINT

pwd

2.3.3 Creating a new file

Let’s create a new file called myfile.txt by launching the text editor nano:

nano myfile.txt

Now inside the nano screen:

  1. Write some text

  2. Exit the “writing mode” with ctrl+x nano

  3. To save the file, type y and hit “Enter”

  4. Confirm the name of the file and hit “Enter”

List the contents of the folder. Can you see the file we have just created?

2.3.4 Copying, renaming, moving and deleting files

First let’s create a new folder called myfolder. Do you remember how to do this?

HINT

mkdir myfolder

And now let’s make a copy of myfile.txt. Here, the command cp expects two arguments, and the order of these arguments matter. The first is the name of the file we want to copy, and the second is the name of the new file:

cp myfile.txt newfile.txt

List the contents of the folder. Do you see the new file there?

Now let’s say we want to copy a file and put it inside a folder. In this case, we give the name of the folder as the second argument to cp:

cp myfile.txt myfolder 

# while typing myfold.. try using the TAB to predict the name of the folder!

cp myfile.txt myfolder/  # it will recognise it is a directory and add the / at the end.

List the contents of myfolder. Is myfile.txt there?

ls myfolder

We can also copy the file to another folder and give it a different name, like this:

cp myfile.txt myfolder/copy_of_myfile.txt

List the contents of myfolder again. Do you see two files there?

Instead of copying, we can move files around with the command mv:

mv newfile.txt myfolder

Let’s list the contents of the folders. Where did newfile.txt go?

We can also use the command mv to rename files:

mv myfile.txt myfile_renamed.txt

List the contents of the folder again. What happened to myfile.txt?

Now, let’s say we want to move things from inside myfolder to the current directory. Can you see what the dot (.) is doing in the command below? Let’s try:

mv myfolder/newfile.txt .

Let’s list the contents of the folders. The file newfile.txt was inside myfolder before, where is it now?

The same operation can be done in a different way. In the commands below, can you see what the two dots (.) are doing? Let’s try:

# First we go inside the folder
cd myfolder

# Then we move the file one level up
mv myfile.txt ..

# And then we go back one level
cd ..

Let’s list the contents of the folders. The file myfile.txt was inside myfolder before, where is it now?

To remove files :

rm newfile.txt

Let’s list the contents of the folder. What happened to newfile.txt?

And now let’s delete myfolder:

rm myfolder

It didn’t work did it? An error message came up, what does it mean?

rm: cannot remove ‘myfolder’: Is a directory

To delete a folder we have to modify the command further by adding the flag (-r). Flags are used to pass additional options to the commands:

rm -r myfolder

Let’s list the contents of the folder. What happened to myfolder?

[!warning] In Bash, If you remove the wrong file/directory, it is gone forever!! (no recycle bin!) aka BE CAREFUL!!