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--- | ||
title: Introducing the Shell | ||
teaching: 20 | ||
exercises: 10 | ||
--- | ||
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::::::::::::::::::::::::::::::::::::::: objectives | ||
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- Describe key reasons for learning shell. | ||
- Navigate your file system using the command line. | ||
- Access and read help files for `bash` programs and use help files to identify useful command options. | ||
- Demonstrate the use of tab completion, and explain its advantages. | ||
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:::::::::::::::::::::::::::::::::::::::::::::::::: | ||
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:::::::::::::::::::::::::::::::::::::::: questions | ||
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- What is a command shell and why would I use one? | ||
- How can I move around on my computer? | ||
- How can I see what files and directories I have? | ||
- How can I specify the location of a file or directory on my computer? | ||
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:::::::::::::::::::::::::::::::::::::::::::::::::: | ||
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## What is a shell and why should I care? | ||
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A *shell* is a computer program that presents a command line interface | ||
which allows you to control your computer using commands entered | ||
with a keyboard instead of controlling graphical user interfaces | ||
(GUIs) with a mouse/keyboard/touchscreen combination. | ||
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There are many reasons to learn about the shell: | ||
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- Many bioinformatics tools can only be used through a command line interface. Many more | ||
have features and parameter options which are not available in the GUI. | ||
BLAST is an example. Many of the advanced functions are only accessible | ||
to users who know how to use a shell. | ||
- The shell makes your work less boring. In bioinformatics you often need to repeat tasks with a large number of files. With the shell, you can automate those repetitive tasks and leave you free to do more exciting things. | ||
- The shell makes your work less error-prone. When humans do the same thing a hundred different times | ||
(or even ten times), they're likely to make a mistake. Your computer can do the same thing a thousand times | ||
with no mistakes. | ||
- The shell makes your work more reproducible. When you carry out your work in the command-line | ||
(rather than a GUI), your computer keeps a record of every step that you've carried out, which you can use | ||
to re-do your work when you need to. It also gives you a way to communicate unambiguously what you've done, | ||
so that others can inspect or apply your process to new data. | ||
- Many bioinformatic tasks require large amounts of computing power and can't realistically be run on your | ||
own machine. These tasks are best performed using remote computers or cloud computing, which can only be accessed | ||
through a shell. | ||
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In this lesson you will learn how to use the command line interface to move around in your file system. | ||
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## How to access the shell | ||
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On a Mac or Linux machine, you can access a shell through a program called "Terminal", which is already available | ||
on your computer. The Terminal is a window into which we will type commands. If you're using Windows, | ||
you'll need to download a separate program to access the shell. | ||
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To save time, we are going to be working on a remote server where all the necessary data and software available. | ||
When we say a 'remote server', we are talking about a computer that is not the one you are working on right now. | ||
You will access the Carpentries remote server where everything is prepared for the lesson. | ||
We will learn the basics of the shell by manipulating some data files. Some of these files are very large | ||
, and would take time to download to your computer. | ||
We will also be using several bioinformatic packages in later lessons and installing all of the software | ||
would take up time even more time. A 'ready-to-go' server lets us focus on learning. | ||
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## How to access the remote server | ||
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You can log-in to the remote server using the [instructions from the Introduction to Cloud Computing for Genomics lesson](https://datacarpentry.org/cloud-genomics/02-logging-onto-cloud#logging-onto-a-cloud-instance). | ||
Your instructor will supply to you the `ip_address` and password that you need to login. | ||
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Each of you will have a different `ip_address`. This will | ||
prevent us from accidentally changing each other's files as we work through the | ||
exercises. The password will be the same for everyone. | ||
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After logging in, you will see a screen showing something like this: | ||
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```output | ||
Welcome to Ubuntu 20.04.5 LTS (GNU/Linux 5.4.0-137-generic x86_64) | ||
* Documentation: https://help.ubuntu.com | ||
* Management: https://landscape.canonical.com | ||
* Support: https://ubuntu.com/advantage | ||
System information as of Mon 13 Mar 2023 03:57:46 AM UTC | ||
System load: 0.0 Processes: 192 | ||
Usage of /: 20.3% of 98.27GB Users logged in: 0 | ||
Memory usage: 25% IPv4 address for eth0: 172.31.12.214 | ||
Swap usage: 0% | ||
Get cloud support with Ubuntu Advantage Cloud Guest: | ||
http://www.ubuntu.com/business/services/cloud | ||
178 updates can be applied immediately. | ||
108 of these updates are standard security updates. | ||
To see these additional updates run: apt list --upgradable | ||
Last login: Fri Mar 10 03:14:44 2023 from 72.83.168.14 | ||
``` | ||
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This provides a lot of information about the remote server that you're logging into. We're not going to use most of this information for | ||
our workshop, so you can clear your screen using the `clear` command. | ||
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Type the word `clear` into the terminal and press the `Enter` key. | ||
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```bash | ||
$ clear | ||
``` | ||
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This will scroll your screen down to give you a fresh screen and will make it easier to read. | ||
You haven't lost any of the information on your screen. If you scroll up, you can see everything that has been output to your screen | ||
up until this point. | ||
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::::::::::::::::::::::::::::::::::::::::: callout | ||
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## Tip | ||
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Hot-key combinations are shortcuts for performing common commands. | ||
The hot-key combination for clearing the console is `Ctrl+L`. Feel free to try it and see for yourself. | ||
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:::::::::::::::::::::::::::::::::::::::::::::::::: | ||
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## Navigating your file system | ||
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The part of the operating system that manages files and directories | ||
is called the **file system**. | ||
It organizes our data into files, | ||
which hold information, | ||
and directories (also called "folders"), | ||
which hold files or other directories. | ||
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Several commands are frequently used to create, inspect, rename, and delete files and directories. | ||
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::::::::::::::::::::::::::::::::::::::::: callout | ||
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## Preparation Magic | ||
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You may have a prompt (the characters to the left of the cursor) that looks different from the `$` sign character used here. | ||
If you would like to change your prompt to match the example prompt, first type the command: | ||
`echo $PS1` | ||
into your shell, followed by pressing the <kbd>Enter</kbd> key. | ||
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This will print the bash special characters that are currently defining your prompt. | ||
To change the prompt to a `$` (followed by a space), enter the command: | ||
`PS1='$ '` | ||
Your window should look like our example in this lesson. | ||
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To change back to your original prompt, type in the output of the previous command `echo $PS1` (this will be different depending on the | ||
original configuration) between the quotes in the following command: | ||
`PS1=""` | ||
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For example, if the output of `echo $PS1` was `\u@\h:\w $ `, | ||
then type those characters between the quotes in the above command: `PS1="\u@\h:\w $ "`. | ||
Alternatively, you can reset your original prompt by exiting the shell and opening a new session. | ||
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This isn't necessary to follow along (in fact, your prompt may have other helpful information you want to know about). This is up to you! | ||
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:::::::::::::::::::::::::::::::::::::::::::::::::: | ||
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```bash | ||
$ | ||
``` | ||
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The dollar sign is a **prompt**, which shows us that the shell is waiting for input; | ||
your shell may use a different character as a prompt and may add information before | ||
the prompt. When typing commands, either from these lessons or from other sources, | ||
do not type the prompt, only the commands that follow it. | ||
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Let's find out where we are by running a command called `pwd` | ||
(which stands for "print working directory"). | ||
At any moment, our **current working directory** | ||
is our current default directory, | ||
i.e., | ||
the directory that the computer assumes we want to run commands in, | ||
unless we explicitly specify something else. | ||
Here, | ||
the computer's response is `/home/dcuser`, | ||
which is the top level directory within our cloud system: | ||
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```bash | ||
$ pwd | ||
``` | ||
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```output | ||
/home/dcuser | ||
``` | ||
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Let's look at how our file system is organized. We can see what files and subdirectories are in this directory by running `ls`, | ||
which stands for "listing": | ||
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```bash | ||
$ ls | ||
``` | ||
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```output | ||
R r_data shell_data | ||
``` | ||
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`ls` prints the names of the files and directories in the current directory in | ||
alphabetical order, | ||
arranged neatly into columns. | ||
We'll be working within the `shell_data` subdirectory, and creating new subdirectories, throughout this workshop. | ||
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The command to change locations in our file system is `cd`, followed by a | ||
directory name to change our working directory. | ||
`cd` stands for "change directory". | ||
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Let's say we want to navigate to the `shell_data` directory we saw above. We can | ||
use the following command to get there: | ||
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```bash | ||
$ cd shell_data | ||
``` | ||
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Let's look at what is in this directory: | ||
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```bash | ||
$ ls | ||
``` | ||
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```output | ||
sra_metadata untrimmed_fastq | ||
``` | ||
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We can make the `ls` output more comprehensible by using the **flag** `-F`, | ||
which tells `ls` to add a trailing `/` to the names of directories: | ||
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```bash | ||
$ ls -F | ||
``` | ||
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```output | ||
sra_metadata/ untrimmed_fastq/ | ||
``` | ||
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Anything with a "/" after it is a directory. Things with a "\*" after them are programs. If | ||
there are no decorations, it's a file. | ||
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`ls` has lots of other options. To find out what they are, we can type: | ||
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```bash | ||
$ man ls | ||
``` | ||
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`man` (short for manual) displays detailed documentation (also referred as man page or man file) | ||
for `bash` commands. It is a powerful resource to explore `bash` commands, understand | ||
their usage and flags. Some manual files are very long. You can scroll through the | ||
file using your keyboard's down arrow or use the <kbd>Space</kbd> key to go forward one page | ||
and the <kbd>b</kbd> key to go backwards one page. When you are done reading, hit <kbd>q</kbd> | ||
to quit. | ||
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::::::::::::::::::::::::::::::::::::::: challenge | ||
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## Challenge | ||
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Use the `-l` option for the `ls` command to display more information for each item | ||
in the directory. What is one piece of additional information this long format | ||
gives you that you don't see with the bare `ls` command? | ||
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::::::::::::::: solution | ||
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## Solution | ||
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```bash | ||
$ ls -l | ||
``` | ||
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```output | ||
total 8 | ||
drwxr-x--- 2 dcuser dcuser 4096 Jul 30 2015 sra_metadata | ||
drwxr-xr-x 2 dcuser dcuser 4096 Nov 15 2017 untrimmed_fastq | ||
``` | ||
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The additional information given includes the name of the owner of the file, | ||
when the file was last modified, and whether the current user has permission | ||
to read and write to the file. | ||
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::::::::::::::::::::::::: | ||
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:::::::::::::::::::::::::::::::::::::::::::::::::: | ||
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No one can possibly learn all of these arguments, that's what the manual page | ||
is for. You can (and should) refer to the manual page or other help files | ||
as needed. | ||
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Let's go into the `untrimmed_fastq` directory and see what is in there. | ||
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```bash | ||
$ cd untrimmed_fastq | ||
$ ls -F | ||
``` | ||
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```output | ||
SRR097977.fastq SRR098026.fastq | ||
``` | ||
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This directory contains two files with `.fastq` extensions. FASTQ is a format | ||
for storing information about sequencing reads and their quality. | ||
We will be learning more about FASTQ files in a later lesson. | ||
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### Shortcut: Tab Completion | ||
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Typing out file or directory names can waste a | ||
lot of time and it's easy to make typing mistakes. Instead we can use tab complete | ||
as a shortcut. When you start typing out the name of a directory or file, then | ||
hit the <kbd>Tab</kbd> key, the shell will try to fill in the rest of the | ||
directory or file name. | ||
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Return to your home directory: | ||
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```bash | ||
$ cd | ||
``` | ||
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then enter: | ||
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```bash | ||
$ cd she<tab> | ||
``` | ||
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The shell will fill in the rest of the directory name for | ||
`shell_data`. | ||
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Now change directories to `untrimmed_fastq` in `shell_data` | ||
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```bash | ||
$ cd shell_data | ||
$ cd untrimmed_fastq | ||
``` | ||
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Using tab complete can be very helpful. However, it will only autocomplete | ||
a file or directory name if you've typed enough characters to provide | ||
a unique identifier for the file or directory you are trying to access. | ||
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For example, if we now try to list the files which names start with `SR` | ||
by using tab complete: | ||
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```bash | ||
$ ls SR<tab> | ||
``` | ||
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The shell auto-completes your command to `SRR09`, because all file names in | ||
the directory begin with this prefix. When you hit | ||
<kbd>Tab</kbd> again, the shell will list the possible choices. | ||
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```bash | ||
$ ls SRR09<tab><tab> | ||
``` | ||
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```output | ||
SRR097977.fastq SRR098026.fastq | ||
``` | ||
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Tab completion can also fill in the names of programs, which can be useful if you | ||
remember the beginning of a program name. | ||
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```bash | ||
$ pw<tab><tab> | ||
``` | ||
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```output | ||
pwck pwconv pwd pwdx pwunconv | ||
``` | ||
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Displays the name of every program that starts with `pw`. | ||
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## Summary | ||
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We now know how to move around our file system using the command line. | ||
This gives us an advantage over interacting with the file system through | ||
a GUI as it allows us to work on a remote server, carry out the same set of operations | ||
on a large number of files quickly, and opens up many opportunities for using | ||
bioinformatic software that is only available in command line versions. | ||
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In the next few episodes, we'll be expanding on these skills and seeing how | ||
using the command line shell enables us to make our workflow more efficient and reproducible. | ||
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:::::::::::::::::::::::::::::::::::::::: keypoints | ||
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- The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI. | ||
- Useful commands for navigating your file system include: `ls`, `pwd`, and `cd`. | ||
- Most commands take options (flags) which begin with a `-`. | ||
- Tab completion can reduce errors from mistyping and make work more efficient in the shell. | ||
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:::::::::::::::::::::::::::::::::::::::::::::::::: | ||
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