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First steps
Our main goal is to set up everyone clients, and to get the main tools to work in the future sessions: ability to connect to the remote server, using screen to keep a living session on the remote server.
- Read carefully each paragraph before typing commands.
- Use the TAB completion. Always.
- Strictly follow the instructions using the suggested filenames: creativity is not a positive quality for Bash beginners ;)
Follow instructors instructions to log in into your machine. Generally speaking you need to know:
- The address of the remote machine (can be an IP like 44.20.200.12 or a string like server4 or nasa.org)
- Your username
- Your password
Review the page on 🔗 remote access for further details.
By default, when you log into a remote machine, you'll find yourself welcomed in your home directory. This is a special location dedicated to you, where you can save some files. On a typical set up its path will be /home/username/
, but on complex servers, with many users, this can vary widely. To check your location, use the pwd
(print working directory) command:
pwd
Remember that the output will be the absolute path of your current location.
While it might sound strange to have identity problems at your young age, if you use multiple machines it could be that you have more usernames. So if you are unsure about who you are (i.e. what is your current active username):
whoami
To quickly go (or return) to our home directory, the command is simply:
cd
Create an empty file with your name in your home using the touch command:
touch ~/AndreaTelatin.txt
After going to our home, let's download the exercise files from the repository with this command:
git clone https://github.com/telatin/learn_bash.git
Did we download something? Try the ls (list) command to see:
ls
We can also add a first switch to this command: to view more details use the -l (long) switch:
ls -l
What does the learn_bash directory contains?
ls -l learn_bash
Now that you tried the first commands, let's make a step back. The linux shell has a string to tell you it's ready to receive commands. The string is called shell prompt, and can be very minimal, like a simple $, or a more complex thing. As you can guess, it's something we can customize. Usually has a structure like:
telatin@gmh:~$
That is: username
@ machine name
: current directory
$
The last character is conventionally a dollar sign ($) for regular users, and a sharp (#) for super-user (administrators). In Linux there is only one administrator called root, but some users could have the privilege to impersonate root from time to time.
Also note that the tilda (~) is a shortcut for your home directory.
Remember that you have to wait to see the shell prompt before issuing new commands. If you don't see it, maybe the previous command is stuck or simply still working.
Before moving on with the workshop, we will start using a powerful program for a safer and better work on a remote server: screen.
Assuming you never used screen on the server, you can create a new session using the command:
screen -S course
More details on this: Using screen tutorial or view a video on this
Now try changing directory, that means setting a new working directory:
cd /tmp
To return quickly to the home directory, you can use cd
without specifying the destination path:
cd
Now we are back to our home directory. So we can create a new sub-directory called course:
mkdir course
More details on this, but we'll make more examples on Day2: Introduction to the filesystem Using the manual for a command
Bundled with your distribution there is a manual. It's useful to know that is there, but it's even more useful understanding how to use it as we'll see that another very handy shell command has the very same behaviour.
The manual command is man, followed by the command:
man ls
When launching the manual, you'll enter an interactive page. You can:
- Scroll using the arrow keys, or “Page Up” and “Page down”, or the space bar to scroll down one page
-
g
will go quickly to the beginning of the document,G
to the end -
/
enable a serch inside the document: type “/”, a string and then ENTER. - After a search
n
will jump to the next occurrence,N
to the previous. - Finally,
q
to quit
· Bioinformatics at the Command Line - Andrea Telatin, 2017-2020
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