source commit: 86cbe9d

Author: actions-user

01-introduction.md

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+---
+title: Navigating Files and Directories
+teaching: 30
+exercises: 20
+---
+
+::::::::::::::::::::::::::::::::::::::: objectives
+
+- Use a single command to navigate multiple steps in your directory structure, including moving backwards (one level up).
+- Perform operations on files in directories outside your working directory.
+- Work with hidden directories and hidden files.
+- Interconvert between absolute and relative paths.
+- Employ navigational shortcuts to move around your file system.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: questions
+
+- How can I perform operations on files outside of my working directory?
+- What are some navigational shortcuts I can use to make my work more efficient?
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Moving around the file system
+
+We've learned how to use `pwd` to find our current location within our file system.
+We've also learned how to use `cd` to change locations and `ls` to list the contents
+of a directory. Now we're going to learn some additional commands for moving around
+within our file system.
+
+Use the commands we've learned so far to navigate to the `shell_data/untrimmed_fastq` directory, if
+you're not already there.
+
+```bash
+$ cd
+$ cd shell_data
+$ cd untrimmed_fastq
+```
+
+What if we want to move back up and out of this directory and to our top level
+directory? Can we type `cd shell_data`? Try it and see what happens.
+
+```bash
+$ cd shell_data
+```
+
+```output
+-bash: cd: shell_data: No such file or directory
+```
+
+Your computer looked for a directory or file called `shell_data` within the
+directory you were already in. It didn't know you wanted to look at a directory level
+above the one you were located in.
+
+We have two special directory names `.` and `..`; `.` refers to the current directory you are in and `..` refers to the directory one level above the current directory. We can use `..` with `cd` to move up one directory level.
+
+```bash
+$ cd ..
+```
+
+Now we can use `pwd` to make sure that we are in the directory we intended to navigate
+to, and `ls` to check that the contents of the directory are correct.
+
+```bash
+$ pwd
+```
+
+```output
+/home/dcuser/shell_data
+```
+
+```bash
+$ ls
+```
+
+```output
+sra_metadata  untrimmed_fastq
+```
+
+From this output, we can see that `..` did indeed take us back one level in our file system.
+
+You can chain these together like so:
+
+```bash
+$ ls ../../
+```
+
+prints the contents of `/home`.
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Finding hidden directories
+
+First navigate to the `shell_data` directory. There is a hidden directory within this directory. Explore the options for `ls` to
+find out how to see hidden directories. List the contents of the directory and
+identify the name of the text file in that directory.
+
+Hint: hidden files and folders in Unix start with `.`, for example `.my_hidden_directory`
+
+:::::::::::::::  solution
+
+## Solution
+
+First use the `man` command to look at the options for `ls`.
+
+```bash
+$ man ls
+```
+
+The `-a` option is short for `all` and says that it causes `ls` to "not ignore
+entries starting with ." This is the option we want.
+
+```bash
+$ ls -a
+```
+
+```output
+.  ..  .hidden	sra_metadata  untrimmed_fastq
+```
+
+The name of the hidden directory is `.hidden`. We can navigate to that directory
+using `cd`.
+
+```bash
+$ cd .hidden
+```
+
+And then list the contents of the directory using `ls`.
+
+```bash
+$ ls
+```
+
+```output
+youfoundit.txt
+```
+
+The name of the text file is `youfoundit.txt`.
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+In most commands the flags can be combined together in no particular order to obtain the desired results/output.
+
+```
+$ ls -Fa
+$ ls -laF
+```
+
+## Examining the contents of other directories
+
+By default, the `ls` commands lists the contents of the working
+directory (i.e. the directory you are in). You can always find the
+directory you are in using the `pwd` command. However, you can also
+give `ls` the names of other directories to view. Navigate to your
+home directory if you are not already there.
+
+```bash
+$ cd
+```
+
+Then enter the command:
+
+```bash
+$ ls shell_data
+```
+
+```output
+sra_metadata  untrimmed_fastq
+```
+
+This will list the contents of the `shell_data` directory without
+you needing to navigate there.
+
+The `cd` command works in a similar way.
+
+Try entering:
+
+```bash
+$ cd
+$ cd shell_data/untrimmed_fastq
+```
+
+This will take you to the `untrimmed_fastq` directory without having to go through
+the intermediate directory.
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Navigating practice
+
+Navigate to your home directory. From there, list the contents of the `untrimmed_fastq`
+directory.
+
+:::::::::::::::  solution
+
+## Solution
+
+```bash
+$ cd
+$ ls shell_data/untrimmed_fastq/
+```
+
+```output
+SRR097977.fastq  SRR098026.fastq 
+```
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Full vs. Relative Paths
+
+The `cd` command takes an argument which is a directory
+name. Directories can be specified using either a *relative* path or a
+full *absolute* path. The directories on the computer are arranged into a
+hierarchy. The full path tells you where a directory is in that
+hierarchy. Navigate to the home directory, then enter the `pwd`
+command.
+
+```bash
+$ cd  
+$ pwd  
+```
+
+You will see:
+
+```output
+/home/dcuser
+```
+
+This is the full name of your home directory. This tells you that you
+are in a directory called `dcuser`, which sits inside a directory called
+`home` which sits inside the very top directory in the hierarchy. The
+very top of the hierarchy is a directory called `/` which is usually
+referred to as the *root directory*. So, to summarize: `dcuser` is a
+directory in `home` which is a directory in `/`. More on `root` and
+`home` in the next section.
+
+Now enter the following command:
+
+```bash
+$ cd /home/dcuser/shell_data/.hidden
+```
+
+This jumps forward multiple levels to the `.hidden` directory.
+Now go back to the home directory.
+
+```bash
+$ cd
+```
+
+You can also navigate to the `.hidden` directory using:
+
+```bash
+$ cd shell_data/.hidden
+```
+
+These two commands have the same effect, they both take us to the `.hidden` directory.
+The first uses the absolute path, giving the full address from the home directory. The
+second uses a relative path, giving only the address from the working directory. A full
+path always starts with a `/`. A relative path does not.
+
+A relative path is like getting directions from someone on the street. They tell you to
+"go right at the stop sign, and then turn left on Main Street". That works great if
+you're standing there together, but not so well if you're trying to tell someone how to
+get there from another country. A full path is like GPS coordinates. It tells you exactly
+where something is no matter where you are right now.
+
+You can usually use either a full path or a relative path depending on what is most convenient.
+If we are in the home directory, it is more convenient to enter the full path.
+If we are in the working directory, it is more convenient to enter the relative path
+since it involves less typing.
+
+Over time, it will become easier for you to keep a mental note of the
+structure of the directories that you are using and how to quickly
+navigate amongst them.
+
+:::::::::::::::::::::::::::::::::::::::  challenge
+
+## Relative path resolution
+
+Using the filesystem diagram below, if `pwd` displays `/Users/thing`,
+what will `ls ../backup` display?
+
+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`
+
+![](fig/filesystem-challenge.svg){alt='File System for Challenge Questions'}
+
+:::::::::::::::  solution
+
+## Solution
+
+1. No: there *is* a directory `backup` in `/Users`.
+2. No: this is the content of `Users/thing/backup`,
+  but with `..` we asked for one level further up.
+3. No: see previous explanation.
+  Also, we did not specify `-F` to display `/` at the end of the directory names.
+4. Yes: `../backup` refers to `/Users/backup`.
+
+:::::::::::::::::::::::::
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+### Navigational Shortcuts
+
+The root directory is the highest level directory in your file
+system and contains files that are important for your computer
+to perform its daily work. While you will be using the root (`/`)
+at the beginning of your absolute paths, it is important that you
+avoid working with data in these higher-level directories, as
+your commands can permanently alter files that the operating
+system needs to function. In many cases, trying to run commands
+in `root` directories will require special permissions which are
+not discussed here, so it's best to avoid them and work within your
+home directory. Dealing with the `home` directory is very common.
+The tilde character, `~`, is a shortcut for your home directory.
+In our case, the `root` directory is **two** levels above our
+`home` directory, so `cd` or `cd ~` will take you to
+`/home/dcuser` and `cd /` will take you to `/`. Navigate to the
+`shell_data` directory:
+
+```bash
+$ cd
+$ cd shell_data
+```
+
+Then enter the command:
+
+```bash
+$ ls ~
+```
+
+```output
+R  r_data  shell_data
+```
+
+This prints the contents of your home directory, without you needing to
+type the full path.
+
+The commands `cd`, and `cd ~` are very useful for quickly navigating back to your home directory. We will be using the `~` character in later lessons to specify our home directory.
+
+:::::::::::::::::::::::::::::::::::::::: keypoints
+
+- The `/`, `~`, and `..` characters represent important navigational shortcuts.
+- Hidden files and directories start with `.` and can be viewed using `ls -a`.
+- Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+