A shell is a computer programme that brings operating system services to users or to other programmes as well. The outer layer of the operating system is basically the shell, also known as the user interface. Simply put, it is a kind of software that helps to process or control the commands for Unix programs. It generally controls the commands via the keyboard rather than handling graphical user interfaces (GUIs) from a touchscreen, keyboard, or mouse simultaneously.
The shells in the operating system usually utilize either a graphical user interface or a command-line interface, depending upon the operation that a user wants. This system is named “Shell” because it is considered the outer layer of an operating system. For instance, the default shell in Windows is usually Explorer. The explorer usually allows access to the taskbar, desktop, menu, and other files or functions available accordingly.
How to access the Shell?
A terminal is a program that allows you to access the shell, specifically on Mac and Linux systems. The terminal could be easily seen on your computer. It is basically a window that allows the user to type commands. However, if you are using a Windows operating system, you have to download a program separately to get access to the Shell.
To get access to the shell quickly, you can work on a remote server, as all the required data and software are available on the remote server. Here, “remote server” means the computer, but not the one that you are currently operating.
Listed below is the detailed step-by-step process to access the Shell via remote server:
- First, you need to sign in to the remote server. Furthermore, your instructor will forward you the IP address and password that are required to log in to the remote server.
- Every user will get a different IP address. A different IP address for everyone will prevent any accidental exchange of files by mistake during the whole activity. However, the password details would be similar for every user.
- After filling in the details and signing in, you will see a screen showing something like this:
OUTPUT :
| Welcome to Ubuntu 14.04.3 LTS (GNU/Linux 3.13.0-48-generic x86_64)
* Documentation: https://help.ubuntu.com/ System information as of Sat Feb 2 00:08:17 UTC 2019 System load: 0.0 Memory usage: 5% Processes: 82 Usage of /: 29.9% of 98.30GB Swap usage: 0% Users logged in: 0 Graph this data and manage this system at: https://landscape.canonical.com/ Get cloud support with Ubuntu Advantage Cloud Guest: http://www.ubuntu.com/business/services/cloud 597 packages can be updated. 444 updates are security updates. New release ‘16.04.5 LTS’ available. Run ‘do-release-upgrade’ to upgrade to it. Last login: Fri Feb 1 22:34:53 2019 from c-73-116-43-163.hsd1.ca.comcast.net |
Thus, the above output on screen will offer you all the required information for the remote server that you want to log into. After checking all the details, you can clear your screen by typing the clear command.
- Enter the word clear and press enter;
$ clear
This will clean your screen, give you a new screen, and make it simpler to read. However, if you want to check that info again, scroll up, and the same page will be there for you.
Most importantly, the hot key is the shortcut for easy routes for performing common commands. The combination of hot-keys to clear the control center is Ctrl+L.
Navigating the File system
The file system is the only part of the working system that manages and handles files and folders. It helps to organize your information into files, and those files hold the data and registries.
The characters to the left of the cursor are where you will find the prompt that appears and is highlighted with a unique $sign. However, if you intend to change your prompt to match the model prompt, Then, in your shell, enter the command echo $PS1, and then press the Enter key.
The characters that interpret the prompt will print the bash special characters. If you want to change the prompt to a $, and enter the command: PS1 = “$”.
After that, if there is a need to change the original prompt, type in the result of the last command order echo $PS1. Between the quotes in the following command: PS1=””
For instance, if you get the output as echo “PS1 is u@h:w $, then enter the characters between the phrases in the above command as PS1=”u@h:w $.”
The sign $in prompt usually shows the situation of Shell, as it will be waiting for input. However, it could be possible that your shell might use another character as a prompt. While typing the commands, don’t include the prompt, just enter the commands.
The dollar sign is a prompt. It enables us to understand whether the shell is sitting tight for input; or an alternate person could also be used by the shell as a prompt and may add data before the prompt. When composing orders, either from these examples or from different sources, don’t type the prompt, just the orders that follow it.
Now let’s find the where by running a command called pwd (print working registry). You consider the present working directory as your current default directory. The registry is where the PC expects you to run commands, except if you unequivocally determine something different.
Here, the computer’s result will be /home/dcuser, which is the high-level directory within the cloud system:
$ pwd
OUTPUT :
/home/dcuser
To check how the file system is organized. You can check the file and sub folders in the directory by running ls , which means “listing”
OUTPUT :
R r_data shell_data
If you want to move to the shell_data directory. You can use the command;
CODE
$ cd shell_data
CODE
$ ls
OUTPUT
sra_metadata untrimmed_fastq
With the help of flag -F, you can make the ls output more comprehensible. It will inform ls to add a trailing / to the directories name;
CODE
$ ls -F
OUTPUT
sra_metadata/ untrimmed_fastq/
If you find anything with a / after the directory. The “*” After them would possibly be the programs.
CODE
$ man ls
Man here shows the detailed document for bash commands. It is another amazing source to explore the bash commands and check their usage and flags. Scroll down and use SPACE to go forward on the page. You can use the b key for backward navigation. After completing it, you can quit by hitting the button q.
Now move towards the untrimmed_fastq directory and check it;
CODE
$ cd untrimmed_fastq
$ ls -F
OUTPUT
SRR097977.fastq SRR098026.fastq
This directory consists of two files with .fastq format. The format FASTQ is used for storing information related to sequencing and their quality.
Why do you need to learn about Shell?
Well, as of now, the function of the shell in the computing field must be clarified. However, you must be wondering why you need to learn about Shell. However, there are some solid reasons to learn Shell. Let’s take a closer look at those reasons:
- There are numerous bioinformatics tools that only work via a command line interface. There are certain parameters and options that are not accessible in the GUI, for instance, BLAST. If you know how to deal with Shell, there could be various functions accessible.
- The shell makes your work less exhausting, especially for repetitive tasks. As in bioinformatics, you frequently need to repeat various tasks with an enormous number of files. However, with the help of shell, you can easily automate those repetitive tasks, and it will also free you from these boring tasks.
- Moreover, you can make your work accurate with the shell. It is often seen that when we do the same task hundreds of times, there are more chances of mistakes in it. Whereas, with the help of a shell, your computer can do exactly the same thing multiple times without any errors.
- There is no doubt you can work more productively with the help of shell. When you complete your work in the command line rather than the GUI, your computer saves a record of all steps, which you can use to retry your work if necessary.In short, Shell provides you with a method for imparting unambiguously what you’ve done, with the goal of having others review or apply your process to new information.
- Some certain bioinformatic tasks definitely demand a lot of processing power. And there is no question why not to run your own machine for it. It could be best to perform these tasks using remote computing. For this, you will need the Shell
Conclusion
Overall, you should be aware that the command line is required to move system files. It unquestionably provides an advantage to interact with system files via GUI. However, it also enables users to work on remote servers and perform the same tasks on a large number of files in a short period of time. It also opens up a plethora of opportunities to use bioinformatic software that was previously only available via command line.