Exploring File Systems and Path Navigation

Overview

Questions

• What methods are available for navigating through my computer?
• How can I view the files and directories I possess?
• What are the ways to identify the location of a file or directory on my computer?

Objectives

• Distinguish between a file and a directory, explaining their similarities and differences.
• Convert an absolute path to a relative path and vice versa.
• Create absolute and relative paths to pinpoint specific files and directories.
• Apply options and arguments to alter the behavior of a shell command.
• Show how to use tab completion and discuss its benefits.

The file system is a crucial part of the operating system that manages files and directories. It organizes data into files, which store information, and directories (also known as ‘folders’), which can contain files or other directories.

To manage these files and directories, several commands are commonly used for creation, inspection, renaming, and deletion. We’ll start exploring these by going to our open shell window.

Firstly, let’s determine our current location using the pwd command, which stands for ‘print working directory’. Think of directories as places; at any given moment in the shell, we are situated in one specific place, our current working directory. Most commands operate on files in the current working directory, meaning ‘here’, so it’s crucial to know your location before executing a command. The pwd command helps you identify your current position.

BASH

$ pwd

OUTPUT

/Users/cecil

Here, the computer’s response is /Users/cecil, which is Cecil’s home directory:

Callout

Variations in Home Directory Paths

The appearance of the home directory path varies across different operating systems. For instance, on Linux systems, it typically appears as /home/cecil, whereas on Windows, it might look like C:\Documents and Settings\cecil or C:\Users\cecil. It’s important to note that there can be slight variations in this path depending on the version of Windows you are using. In our future examples, we’ll primarily use outputs from a Mac as a standard reference. Outputs from Linux and Windows may have minor differences but will generally be similar.

We’ll proceed with the assumption that when you execute the pwd command, it shows your user’s home directory. If pwd yields a different result, you might need to navigate to your home directory using the cd command. Otherwise, certain commands in this lesson might not function as described. For additional information on using the cd command to explore other directories, refer to the section Exploring Other Directories.

To grasp the concept of a ‘home directory’, it’s beneficial to first understand the overall structure of the file system. For illustrative purposes, we’ll examine the filesystem on our scientist Cecil’s computer. After this explanation, you’ll learn how to navigate your own filesystem, which will be structured similarly, though not exactly the same.

Here’s an overview of the filesystem on Cecil’s computer:

The filesystem can be visualized as an inverted tree. At the very top is the root directory, which encompasses everything underneath. This root directory is denoted by a solitary slash /; it’s the same slash found at the beginning of /Users/cecil.

Within this root directory are various subdirectories: - bin (housing some built-in programs), - data (for assorted data files), - Users (containing the personal directories of users), - tmp (for temporary files not requiring long-term storage), - among others.

We know that Cecil’s current working directory /Users/cecil is a part of /Users because it appears at the start of its path. Similarly, the presence of the leading / in /Users indicates that it resides within the root directory.

Callout

Understanding the Slash /

It’s important to recognize the dual role of the / character in file paths. When / is positioned at the beginning of a file or directory name, it signifies the root directory. However, when / is found within a path, it serves merely as a separator between different levels in the directory structure.

Under /Users, there are directories for each user with an account on Cecil’s machine, including his colleagues Amelia and Raj.

The files belonging to the user Amelia are located in /Users/amelia, Raj’s files are in /Users/raj, and Cecil’s are in /Users/cecil. In our examples, Cecil is our primary user, so /Users/cecil is our home directory. Usually, when you open a new command prompt, you start in your home directory.

Let’s now learn the command that allows us to view the contents of our filesystem. We can see what’s in our home directory by running ls:

BASH

$ ls

OUTPUT

Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

(Your results might vary slightly based on your operating system and any customizations you’ve made to your filesystem.)

The ls command displays the names of files and directories in the current directory. We can make this output clearer by using the -F option, which instructs ls to add a specific marker to each file and directory name to indicate its type:

• a trailing / signifies a directory
• @ denotes a link
• * marks an executable file

Depending on the settings of your shell, it might also use colors to distinguish files from directories.

BASH

$ ls -F

OUTPUT

Applications/ Documents/    Library/      Music/        Public/
Desktop/      Downloads/    Movies/       Pictures/

Here, we observe that the home directory comprises only sub-directories. Any names in the output lacking a classification symbol are files within the current working directory.

Callout

Tidying Up Your Terminal Screen

When your terminal becomes overly crowded, you can tidy it up with the clear command. This cleans up the screen but doesn’t erase your command history. You can still revisit your past commands by using the ↑ and ↓ keys to navigate through them one line at a time, or by simply scrolling in your terminal.

Discovering Command Help Options

The ls command, like many others, offers a variety of options for its use. To learn about these options and how to utilize a command, there are generally two methods, and the next two sections cover each in turn: the --help option (Linux and Git Bash) and the man command (Linux and macOS). Depending on your system, you might find that only one of them is applicable.

Callout

Assistance with Built-in Bash Commands

Certain commands are integrated directly into the Bash shell and don’t exist as standalone programs in the filesystem. A common example is the cd command, used for changing directories. If you encounter a message such as No manual entry for cd, an alternative is to use help cd. This help command provides guidance on using the Bash built-ins, which are the commands that are part of the shell itself.

The --help option

The majority of Bash commands and programs designed for use in Bash typically support a --help option. This feature provides additional details on how to effectively utilize the command or program.

BASH

$ ls --help

OUTPUT

Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if neither -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options, too.
  -a, --all                  do not ignore entries starting with .
  -A, --almost-all           do not list implied . and ..
      --author               with -l, print the author of each file
  -b, --escape               print C-style escapes for nongraphic characters
      --block-size=SIZE      scale sizes by SIZE before printing them; e.g.,
                               '--block-size=M' prints sizes in units of
                               1,048,576 bytes; see SIZE format below
  -B, --ignore-backups       do not list implied entries ending with ~
  -c                         with -lt: sort by, and show, ctime (time of last
                               modification of file status information);
                               with -l: show ctime and sort by name;
                               otherwise: sort by ctime, newest first
  -C                         list entries by columns
      --color[=WHEN]         colorize the output; WHEN can be 'always' (default
                               if omitted), 'auto', or 'never'; more info below
  -d, --directory            list directories themselves, not their contents
  -D, --dired                generate output designed for Emacs' dired mode
  -f                         do not sort, enable -aU, disable -ls --color
  -F, --classify             append indicator (one of */=>@|) to entries
...        ...        ...

Callout

Handling Unsupported Command-Line Options

When you attempt to use a command-line option that isn’t recognized, commands like ls typically respond with an error message. For example, if you try an unsupported option with ls, it would look something like this:

BASH

$ ls -j

ERROR

ls: invalid option -- 'j'
Try 'ls --help' for more information.

This response indicates that the option you tried is invalid and suggests using the --help option to get more information about the command.

Utilizing the man Command

Another method to learn about ls is by entering the following command:

BASH

$ man ls

Executing this command transforms your terminal into a page displaying a detailed description of the ls command and its various options.

While navigating the man pages, you can move line-by-line using ↑ and ↓. For quicker navigation, B moves up a full page and Spacebar moves down a full page. To search for a specific character or word within the man pages, press / followed by your search term. If your search yields multiple results, you can jump between these occurrences with N (to go forward) and Shift + N (to go backward).

To exit the man pages, simply press Q.

Callout

Accessing Manual Pages Online

Beyond the command-line, there’s a third method to find help for Unix commands: using your web browser to search the internet. When searching online, adding unix man page to your query can lead to more pertinent results.

Additionally, GNU offers a comprehensive collection of manuals online. This includes the core GNU utilities, which provide detailed information on many of the commands discussed in this lesson.

Challenge

Investigating Further Options in ls

Try combining two options together.

What outcome does ls produce with the -l option?

And what happens when you combine the -l option with the -h option?

While some of the information provided by these options, like file permissions and ownership, isn’t covered in this lesson, the remaining details can still be quite informative.

Show me the solution

Using the -l option with ls enables a long format listing. This doesn’t just show the names of files or directories but also additional details like file size and the time of the last modification. When you use -h along with -l, it formats the file size in a ‘human readable’ manner, presenting sizes like 5.3K instead of 5369.

Challenge

Sorting Files by Last Modified in Reverse

Normally, ls sorts the contents of a directory alphabetically by their names. However, if you use ls -t, it sorts files by the time of their last modification, not alphabetically. On the other hand, ls -r displays directory contents in reverse order. What file appears last when you use both the -t and -r options together? Tip: To view the dates of last modifications, you might need to include the -l option.

Exploring ls options on Sagehen HPC: an invalid option error, long and human-readable listings, and time/reverse sorting — note the lab-storage symlinks pointing into /bigdata/lab/.

Show me the solution

When combining -rt with ls, the file that was most recently modified appears at the end of the list. This sorting method is particularly useful for identifying the latest changes you’ve made or for verifying whether a new output file has been created.

Navigating Across Different Directories

ls isn’t limited to just listing the contents of the current working directory. We can also use it to explore the contents of other directories. For example, let’s examine what’s in our Desktop directory by using ls -F Desktop, where ls is the command, -F is an option, and Desktop is the argument. The Desktop argument instructs ls to list contents from a directory other than the current one:

BASH

$ ls -F Desktop

OUTPUT

shell-lesson-data/

If you don’t have a Desktop directory in your current working directory, this command will result in an error. Typically, your home directory contains a Desktop directory, which we assume is the current working directory.

You should see a list of files and sub-directories in your Desktop directory, including the shell-lesson-data directory downloaded earlier. (In most graphical interfaces, the contents of the Desktop directory appear as icons.)

Organizing files into hierarchically structured directories helps keep track of work. Just as piling hundreds of papers on a desk isn’t practical, keeping numerous files in the home directory can be equally chaotic.

Knowing that shell-lesson-data is on our Desktop, we can do two things:

First, we can view its contents with ls, passing the directory name as an argument:

BASH

$ ls -F Desktop/shell-lesson-data

OUTPUT

exercise-data/  gobekli-tepe-excavation/

Second, we can change our current directory. The command cd, followed by a directory name, changes our working directory. cd stands for ‘change directory’. It doesn’t change the directory itself but changes the shell’s setting of our current directory.

To navigate into the exercise-data directory seen above, use these commands:

BASH

$ cd Desktop
$ cd shell-lesson-data
$ cd exercise-data

These commands take us from the home directory to the Desktop, then into shell-lesson-data, and finally into exercise-data. Note that cd doesn’t produce output when successful. Running pwd after cd shows we are now in /Users/cecil/Desktop/shell-lesson-data/exercise-data.

BASH

$ pwd

OUTPUT

/Users/cecil/Desktop/shell-lesson-data/exercise-data

Running ls -F without arguments now lists the contents of /Users/cecil/Desktop/shell-lesson-data/exercise-data:

BASH

$ ls -F

OUTPUT

artifact-catalogs/  excavation-sites/  site-coordinates.txt  pottery-types/  research-notes/

To move up a directory (to its parent), you might think to use cd shell-lesson-data, but this returns an error:

BASH

$ cd shell-lesson-data

ERROR

-bash: cd: shell-lesson-data: No such file or directory

cd only recognizes sub-directories within the current directory. To move up, use:

BASH

$ cd ..

.. is a shorthand for the parent directory. Running pwd after cd .. takes us back to /Users/cecil/Desktop/shell-lesson-data:

BASH

$ pwd

OUTPUT

/Users/cecil/Desktop/shell-lesson-data

To see .. in the ls output, use the -a option with ls -F:

BASH

$ ls -F -a

OUTPUT

./  ../  exercise-data/  gobekli-tepe-excavation/

-a (show all) reveals files and directories starting with ., such as .. (the parent directory). It also shows . (the current directory). These shortcuts are useful in many scenarios.

Remember, command line tools often allow combining multiple options into a single -, like ls -F -a being equivalent to ls -Fa.

Callout

Encountering Hidden Files

Beyond the special directories .. (parent directory) and . (current directory), you might encounter a file named .bash_profile. This file typically holds configuration settings for the shell. Additionally, there might be other files and directories starting with .. These are commonly configuration files for various programs on your computer. The ., or dot prefix, is a convention used to keep these configuration files hidden from view in standard directory listings, helping to keep your terminal view uncluttered when you use the basic ls command.

The fundamental commands for navigating your computer’s filesystem are pwd, ls, and cd. Let’s delve into some variations of these commands. What happens if you enter cd without specifying a directory?

BASH

$ cd

To verify what just occurred, use pwd:

BASH

$ pwd

OUTPUT

/Users/cecil

It turns out that entering cd without any argument takes you back to your home directory. This is a quick way to return to a familiar location if you find yourself lost within your filesystem.

Now, let’s go back to the exercise-data directory we were in earlier. Previously, we navigated there using three separate commands, but we can actually reach exercise-data directly in a single step:

BASH

$ cd Desktop/shell-lesson-data/exercise-data

Verify your current location by running pwd and ls -F.

To move up one level from the exercise-data directory, we could use cd .., but there’s another method to navigate to any directory, irrespective of your current position.

Until now, we’ve been using relative paths for specifying directories. When a command like ls or cd is paired with a relative path, it seeks that location from our current spot, not from the filesystem’s root.

Alternatively, you can specify a directory’s absolute path, which includes its full path starting from the root directory. An absolute path is indicated by a leading slash (/). This slash directs the system to trace the path from the filesystem’s root, ensuring the path is unique regardless of your current directory.

This method allows us to go back to our shell-lesson-data directory from any location in the filesystem, including from within exercise-data. To determine the absolute path you need, use pwd to find your current location and then navigate to shell-lesson-data.

BASH

$ pwd

OUTPUT

/Users/cecil/Desktop/shell-lesson-data/exercise-data

BASH

$ cd /Users/cecil/Desktop/shell-lesson-data

Confirm your current directory by running pwd and ls -F, making sure you’re where you intended to be.

Callout

Two Useful Navigation Shortcuts

The shell uses the tilde (~) at the start of a path to represent “the current user’s home directory”. For instance, if Cecil’s home directory is /Users/cecil, then ~/data would be the same as /Users/cecil/data. Remember, this shortcut only works when it’s the first character in the path; a path like here/there/~/elsewhere does not resolve to here/there/Users/cecil/elsewhere.

Another handy shortcut is the - (dash) character. When used with cd, it means the last directory you were in. This is a quick way to switch back and forth between two directories. For example, if you use cd - twice in a row, you’ll return to your original directory.

It’s important to note the difference between cd .. and cd -: the former moves you up one directory level, while the latter takes you back to your previous location.

---

Give it a try! First, navigate to ~/Desktop/shell-lesson-data (you should already be there).

BASH

$ cd ~/Desktop/shell-lesson-data

Next, move into the exercise-data/pottery-types directory:

BASH

$ cd exercise-data/pottery-types

Now, if you execute:

BASH

$ cd -

you’ll find yourself back in ~/Desktop/shell-lesson-data. If you run cd - once more, you’ll return to ~/Desktop/shell-lesson-data/exercise-data/pottery-types.

Challenge

Navigating with Absolute and Relative Paths

If Amanda is currently in /Users/amelia/data, which of the following commands can she use to return to her home directory, /Users/amelia?

1. cd .
2. cd /
3. cd /home/amelia
4. cd ../..
5. cd ~
6. cd home
7. cd ~/data/..
8. cd
9. cd ..

Show me the solution

1. No: . denotes the current directory.
2. No: / is the root directory of the filesystem.
3. No: Amanda’s home directory is /Users/amelia, not /home/amelia.
4. Yes: Moves up two levels, placing her in /Users, one level above her home directory.
5. Yes: ~ is a shortcut for the user’s home directory, /Users/amelia in this case.
6. No: This attempts to access a home directory within the current directory, not the user’s home.
7. Yes: A roundabout method, but it effectively moves to ~/data then up one level to ~/.
8. Yes: A direct shortcut to the user’s home directory.
9. Yes: Moves up one directory level to /Users/amelia.

Challenge

Understanding Relative Path Commands

Referencing the filesystem diagram provided, if the current directory shown by pwd is /Users/thing, what output will the command ls -F ../backup produce?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original/ pnas_final/ pnas_sub/

Show me the solution

1. No: There is indeed a backup directory at /Users.
2. No: These are the contents of /Users/thing/backup, but .. goes one level up.
3. No: Same as above; .. takes us to a higher directory level.
4. Yes: ../backup/ refers to the backup directory at /Users/backup/.

Challenge

Understanding ls with Reverse Order

Consider the filesystem diagram provided. If pwd shows /Users/backup, and the -r option makes ls list items in reverse order, which command(s) would produce the following output?

OUTPUT

pnas_sub/ pnas_final/ original/

1. ls pwd 2. ls -r -F 3. ls -r -F /Users/backup

Show me the solution

1. No: pwd is not a directory, but a command that prints the working directory.
2. Yes: Using ls without a directory argument lists the contents of the current directory in reverse order.
3. Yes: This explicitly specifies the absolute path to list in reverse order.

Breaking Down a Shell Command’s Structure

---

As we delve deeper into shell commands, options, and arguments, it’s beneficial to clarify some terminology using a structured approach.

Let’s examine the following example of a shell command and dissect its components:

BASH

$ ls -F /

In this example, ls is the command. It’s accompanied by an option, -F, and an argument, /. Options often begin with a single dash (-), known as short options, or a double dash (--), referred to as long options. [Options] modify how a command operates, while Arguments specify the objects (like files or directories) the command should act upon. Sometimes, both options and arguments are collectively called parameters. Commands can be used with multiple options and arguments, but they don’t always need to have either.

Options are sometimes called switches or flags, especially when they don’t require an additional argument. In this lesson, however, we’ll stick to the term option.

Spacing is crucial: each part of the command is separated by spaces. Forgetting a space, like writing ls-F, makes the shell look for a command that doesn’t exist. Also, be aware that capitalization matters. For instance, ls -s shows the size of files, whereas ls -S sorts files by size. Here’s an example:

BASH

$ cd ~/Desktop/shell-lesson-data
$ ls -s exercise-data

OUTPUT

total 28
 4 artifact-catalogs   4 excavation-sites  12 site-coordinates.txt   4 pottery-types   4 research-notes

Note that ls -s shows sizes in blocks, which vary between different operating systems, so your output might differ from the example.

BASH

$ ls -S exercise-data

OUTPUT

artifact-catalogs  excavation-sites  pottery-types  research-notes  site-coordinates.txt

To summarize, our command ls -F / provides a list of files and directories in the root directory /. An example output from this command could be:

BASH

$ ls -F /

OUTPUT

Applications/         System/
Library/              Users/
Network/              Volumes/

Callout

Deciding Between Short and Long Command Options

When you have the choice of using either short or long options for command-line operations:

• When typing commands directly into the shell, use short options. This strategy minimizes keystrokes and speeds up your workflow.
• For scripting purposes, lean towards long options. They provide better clarity and enhance readability, which is crucial as scripts are typically read more frequently than they are written.

Cecil’s Pipeline: File Organization

With his knowledge of files and directories, Cecil is set to organize the upcoming files from the protein assay machine.

He creates a directory named gobekli-tepe-excavation, reminding him of the data’s origin. This directory will house both the data files from the assay machine and his data processing scripts.

Each of Cecil’s samples carries a unique ten-character ID following his lab’s system, such as ‘NENE01729A’. He utilized this ID in his collection log to note the sample’s location, time and other details. Thus, he decides to incorporate these IDs into the filenames of each data file. Given that the assay machine outputs plain text, he names his files NENE01729A.txt, NENE01812A.txt, and so on, with all 1520 files going into the same directory.

Now, in his current directory shell-lesson-data, Cecil can view his files with the command:

BASH

$ ls gobekli-tepe-excavation/

While this command is a bit lengthy, Cecil can use tab completion to let the shell do most of the typing. If he types:

BASH

$ ls gob

and presses Tab, the shell completes the directory name:

BASH

$ ls gobekli-tepe-excavation/

Pressing Tab again doesn’t change the output, as multiple possibilities exist. However, pressing Tab twice will list all the files.

If Cecil then types a and presses Tab, the shell will add ‘ancient’ because both script names start with those characters:

BASH

$ ls gobekli-tepe-excavation/ancient

To display these files, he can press Tab twice again:

BASH

ls gobekli-tepe-excavation/ancient
ancientdiff.sh   ancientstats.sh

This feature is known as tab completion and is a common convenience across many shell tools.

Key Points

• The file system is responsible for managing information on the disk.
• Information is stored in files, which are stored in directories (folders).
• Directories can also store other directories, which then form a directory tree.
• pwd prints the user’s current working directory.
• ls [path] prints a listing of a specific file or directory; ls on its own lists the current working directory.
• cd [path] changes the current working directory.
• Most commands take options that begin with a single -.
• Directory names in a path are separated with / on Unix, but \ on Windows.
• / on its own is the root directory of the whole file system.
• An absolute path specifies a location from the root of the file system.
• A relative path specifies a location starting from the current location.
• . on its own means ‘the current directory’; .. means ‘the directory above the current one’.