Course Logistics and Getting to know people

Overview

Teaching: 30 min
Exercises: 0 min

Questions

Who are you?

Who are we?

Where are we going? 🧭

Objectives

Get to know each other and feel comfortable.

Using Software Carpentry

The lessons are in episodes.

I will try to keep to time. I may jump some bits. Don’t worry; you can get at the materials and you can ask us after the course has finished.

Zoom and Slack

We use zoom for the main lesson, and breakout rooms for the exercises and help.

Key Points

Course logistics.

Introducing the Shell

Overview

Teaching: 15 min
Exercises: 0 min

Questions

What is a command shell and why would I use one?

Objectives

Explain how the shell relates to the keyboard, the screen, the operating system, and users’ programs.

Explain when and why command-line interfaces should be used instead of graphical interfaces.

Background

Humans and computers commonly interact in many different ways, such as through a keyboard and mouse, touch screen interfaces, or using speech recognition systems. The most widely used way to interact with personal computers is called a graphical user interface (GUI). With a GUI, we give instructions by clicking a mouse and using menu-driven interactions.

While the visual aid of a GUI makes it intuitive to learn, this way of delivering instructions to a computer scales very poorly. Imagine the following task: for a literature search, you have to copy the third line of one thousand text files in one thousand different directories and paste it into a single file. Using a GUI, you would not only be clicking at your desk for several hours, but you could potentially also commit an error in the process of completing this repetitive task. This is where we take advantage of the Unix shell. The Unix shell is both a command-line interface (CLI) and a scripting language, allowing such repetitive tasks to be done automatically and fast. With the proper commands, the shell can repeat tasks with or without some modification as many times as we want. Using the shell, the task in the literature example can be accomplished in seconds.

Most of how shell works is inherited from a time before the GUI!

The Shell

The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs like climate modeling software or simple commands that create an empty directory with only one line of code. The most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that provide Unix-like tools for Windows.

Using the shell will take some effort and some time to learn. While a GUI presents you with choices to select, CLI choices are not automatically presented to you, so you must learn a few commands like new vocabulary in a language you’re studying. However, unlike a spoken language, a small number of “words” (i.e. commands) gets you a long way, and we’ll cover those essential few today.

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of data automatically. Sequences of commands can be written into a script, improving the reproducibility of workflows.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers, including JASMIN. Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-performance computing systems. As clusters and cloud computing systems become more popular for scientific data crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line skills covered here to tackle a wide range of scientific questions and computational challenges.

Let’s get started.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $ . Most importantly: when typing commands, either from these lessons or from other sources, do not type the prompt, only the commands that follow it. Also note that after you type a command, you have to press the Enter key to execute it.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text editor program, for example.

So let’s try our first command, ls which is short for listing. This command will list the contents of the current directory:

$ ls

Desktop     Downloads   Movies      Pictures
Documents   Library     Music       Public

When you log into JASMIN, your current directory will be your home directory on JASMIN (until you change to a different directory). The contents are unlikely to be the same as in the above example, but you will see whatever files you have in that directory. (With a brand new JASMIN account, maybe there won’t yet be any files for ls to show you.)

Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:
$ ks
ks: command not found
This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

Nelle’s Pipeline: A Typical Problem

Nelle Nemo, a marine biologist, has just returned from a six-month survey of the North Pacific Gyre, where she has been sampling gelatinous marine life in the Great Pacific Garbage Patch. She has 1520 samples that she’s run through an assay machine to measure the relative abundance of 300 proteins. She needs to run these 1520 files through an imaginary program called goostats.sh she inherited. On top of this huge task, she has to write up results by the end of the month so her paper can appear in a special issue of Aquatic Goo Letters.

The bad news is that if she has to run goostats.sh by hand using a GUI, she’ll have to select and open a file 1520 times. If goostats.sh takes 30 seconds to run each file, the whole process will take more than 12 hours of Nelle’s attention. With the shell, Nelle can instead assign her computer this mundane task while she focuses her attention on writing her paper.

The next few lessons will explore the ways Nelle can achieve this. More specifically, they explain how she can use a command shell to run the goostats.sh program, using loops to automate the repetitive steps of entering file names, so that her computer can work while she writes her paper.

As a bonus, once she has put a processing pipeline together, she will be able to use it again whenever she collects more data.

In order to achieve her task, Nelle needs to know how to:

navigate to a file/directory
create a file/directory
check the length of a file
chain commands together
retrieve a set of files
iterate over files
run a shell script containing her pipeline

Key Points

A shell is a program whose primary purpose is to read commands and run other programs.

This lesson uses Bash, the default shell in many implementations of Unix.

Programs can be run in Bash by entering commands at the command-line prompt.

The shell’s main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.

The shell’s main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.

Navigating Files and Directories

Overview

Teaching: 25 min
Exercises: 15 min

Questions

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?

Objectives

Explain the similarities and differences between a file and a directory.

Translate an absolute path into a relative path and vice versa.

Construct absolute and relative paths that identify specific files and directories.

Use options and arguments to change the behaviour of a shell command.

Demonstrate the use of tab completion and explain its advantages.

The part of the operating system responsible for managing 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.

Several commands are frequently used to create, inspect, rename, and delete files and directories. To start exploring them, we’ll go to our open shell window.

First, let’s find out where we are by running a command called pwd (which stands for ‘print working directory’). Directories are like places — at any time while we are using the shell, we are in exactly one place called our current working directory. Commands mostly read and write files in the current working directory, i.e. ‘here’, so knowing where you are before running a command is important. pwd shows you where you are:

$ pwd

/Users/nelle

Here, the computer’s response is /Users/nelle, which is Nelle’s home directory:

Home Directory Variation

The home directory path will look different on different operating systems. On Linux, it may look like /home/nelle, and on Windows, it will be similar to C:\Documents and Settings\nelle or C:\Users\nelle. (Note that it may look slightly different for different versions of Windows.) In future examples, we’ve used Mac output as the default - Linux and Windows output may differ slightly but should be generally similar.

On JASMIN, users’ home directories are under /home/users.

We will also assume that your pwd command returns your user’s home directory. If pwd returns something different, you may need to navigate there using cd or some commands in this lesson will not work as written. See Exploring Other Directories for more details on the cd command.

To understand what a ‘home directory’ is, let’s have a look at how the file system as a whole is organized. For the sake of this example, we’ll be illustrating the filesystem on our scientist Nelle’s computer. After this illustration, you’ll be learning commands to explore your own filesystem, which will be constructed in a similar way, but not be exactly identical.

On Nelle’s computer, the filesystem looks like this:

The file system is made up of a root directory that contains sub-directories
titled bin, data, users, and tmp

At the top is the root directory that holds everything else. We refer to it using a slash character, /, on its own; this character is the leading slash in /Users/nelle.

Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (for miscellaneous data files), Users (where users’ personal directories are located), tmp (for temporary files that don’t need to be stored long-term), and so on.

We know that our current working directory /Users/nelle is stored inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.

Slashes

Notice that there are two meanings for the / character. When it appears at the front of a file or directory name, it refers to the root directory. When it appears inside a path, it’s just a separator.

Underneath /Users, we find one directory for each user with an account on Nelle’s machine, her colleagues imhotep and larry.

Like other directories, home directories are sub-directories underneath
"/Users" like "/Users/imhotep", "/Users/larry" or
"/Users/nelle"

The user imhotep’s files are stored in /Users/imhotep, user larry’s in /Users/larry, and Nelle’s in /Users/nelle. Because Nelle is the user in our examples here, therefore we get /Users/nelle as our home directory. Typically, when you open a new command prompt, you will be in your home directory to start.

Now let’s learn the command that will let us see the contents of our own filesystem. We can see what’s in our home directory by running ls:

$ ls

Applications Documents    Library      Music        Public
Desktop      Downloads    Movies       Pictures

(Again, your results may be slightly different depending on your operating system and how you have customized your filesystem.)

ls prints the names of the files and directories in the current directory. We can make its output more comprehensible by using the -F option which tells ls to classify the output by adding a marker to file and directory names to indicate what they are:

a trailing / indicates that this is a directory
@ indicates a link
* indicates an executable

Depending on your shell’s default settings, the shell might also use colors to indicate whether each entry is a file or directory.

$ ls -F

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

Here, we can see that our home directory contains only sub-directories. Any names in our output that don’t have a classification symbol are plain old files.

Clearing your terminal

If your screen gets too cluttered, you can clear your terminal using the clear command. You can still access previous commands using ↑ and ↓ to move line-by-line, or by scrolling in your terminal. You can also clear your terminal by pressing ctrl-L.

Getting help

ls has lots of other options. There are two common ways to find out how to use a command and what options it accepts — depending on your environment, you might find that only one of these ways works:

We can pass a --help option to the command (not available on macOS), such as:
```
 $ ls --help
```
We can read its manual with man (not available in Git Bash), such as:
```
 $ man ls
```

We’ll describe both ways next.

The `--help` option

Most bash commands and programs that people have written to be run from within bash, support a --help option that displays more information on how to use the command or program.

$ ls --help

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
...        ...        ...

Unsupported command-line options

If you try to use an option that is not supported, ls and other commands will usually print an error message similar to:
$ ls -j
ls: invalid option -- 'j'
Try 'ls --help' for more information.

The `man` command

The other way to learn about ls is to type

$ man ls

This command will turn your terminal into a page with a description of the ls command and its options.

To navigate through the man pages, you may use ↑ and ↓ to move line-by-line, or try B and Spacebar to skip up and down by a full page. To search for a character or word in the man pages, use / followed by the character or word you are searching for. Sometimes a search will result in multiple hits. If so, you can move between hits using N (for moving forward) and Shift+N (for moving backward).

To quit the man pages, press Q.

Manual pages on the web

Of course, there is a third way to access help for commands: searching the internet via your web browser. When using internet search, including the phrase unix man page in your search query will help to find relevant results.

GNU provides links to its manuals including the core GNU utilities, which covers many commands introduced within this lesson.

Exploring More ls Flags

You can also use two options at the same time. What does the command ls do when used with the -l option? What about if you use both the -l and the -h option?

Some of its output is about properties that we do not cover in this lesson (such as file permissions and ownership), but the rest should be useful nevertheless.

Solution

The -l option makes ls use a long listing format, showing not only the file/directory names but also additional information, such as the file size and the time of its last modification. If you use both the -h option and the -l option, this makes the file size ‘human readable’, i.e. displaying something like 5.3K instead of 5369.

Listing in Reverse Chronological Order

By default, ls lists the contents of a directory in alphabetical order by name. The command ls -t lists items by time of last change instead of alphabetically. The command ls -r lists the contents of a directory in reverse order. Which file is displayed last when you combine the -t and -r options? Hint: You may need to use the -l option to see the last changed dates.

Solution

The most recently changed file is listed last when using -rt. This can be very useful for finding your most recent edits or checking to see if a new output file was written.

Exploring Other Directories

Not only can we use ls on the current working directory, but we can use it to list the contents of a different directory. Let’s take a look at our Desktop directory by running ls -F Desktop, i.e., the command ls with the -F option and the argument Desktop. The argument Desktop tells ls that we want a listing of something other than our current working directory:

$ ls -F Desktop

shell-lesson-data/

Note that if a directory named Desktop does not exist in your current working directory, this command will return an error. Typically, a Desktop directory exists in your home directory, which we assume is the current working directory of your bash shell.

Your output should be a list of all the files and sub-directories in your Desktop directory, including the shell-lesson-data directory you downloaded at the setup for this lesson. On many systems, the command line Desktop directory is the same as your GUI Desktop. Take a look at your Desktop to confirm that your output is accurate.

As you may now see, using a bash shell is strongly dependent on the idea that your files are organized in a hierarchical file system. Organizing things hierarchically in this way helps us keep track of our work: it’s possible to put hundreds of files in our home directory, just as it’s possible to pile hundreds of printed papers on our desk, but it’s a self-defeating strategy.

Now that we know the shell-lesson-data directory is located in our Desktop directory, we can do two things.

First, we can look at its contents, using the same strategy as before, passing a directory name to ls:

$ ls -F Desktop/shell-lesson-data

exercise-data/  north-pacific-gyre/

Second, we can actually change our location to a different directory, so we are no longer located in our home directory.

The command to change locations is cd followed by a directory name to change our working directory. cd stands for ‘change directory’, which is a bit misleading: the command doesn’t change the directory; it changes the shell’s idea of what directory we are in. The cd command is akin to double-clicking a folder in a graphical interface to get into a folder.

Let’s say we want to move to the data directory we saw above. We can use the following series of commands to get there:

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

These commands will move us from our home directory into our Desktop directory, then into the shell-lesson-data directory, then into the exercise-data directory. You will notice that cd doesn’t print anything. This is normal. Many shell commands will not output anything to the screen when successfully executed. But if we run pwd after it, we can see that we are now in /Users/nelle/Desktop/shell-lesson-data/exercise-data.

If we run ls -F without arguments now, it lists the contents of /Users/nelle/Desktop/shell-lesson-data/exercise-data, because that’s where we now are:

$ pwd

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

$ ls -F

animal-counts/  creatures/  numbers.txt  proteins/  writing/

We now know how to go down the directory tree (i.e. how to go into a subdirectory), but how do we go up (i.e. how do we leave a directory and go into its parent directory)? We might try the following:

$ cd shell-lesson-data

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

But we get an error! Why is this?

With our methods so far, cd can only see sub-directories inside your current directory. There are different ways to see directories above your current location; we’ll start with the simplest.

There is a shortcut in the shell to move up one directory level that looks like this:

$ cd ..

.. is a special directory name meaning “the directory containing this one”, or more succinctly, the parent of the current directory. Sure enough, if we run pwd after running cd .., we’re back in /Users/nelle/Desktop/shell-lesson-data:

$ pwd

/Users/nelle/Desktop/shell-lesson-data

The special directory .. doesn’t usually show up when we run ls. If we want to display it, we can add the -a option to ls -F:

$ ls -F -a

./  ../  exercise-data/  north-pacific-gyre/

-a stands for ‘show all’; it forces ls to show us file and directory names that begin with ., such as .. (which, if we’re in /Users/nelle, refers to the /Users directory). As you can see, it also displays another special directory that’s just called ., which means ‘the current working directory’. It may seem redundant to have a name for it, but we’ll see some uses for it soon.

Note that in most command line tools, multiple options can be combined with a single - and no spaces between the options: ls -F -a is equivalent to ls -Fa.

Other Hidden Files

In addition to the hidden directories .. and ., you may also see a file called .bash_profile. This file usually contains shell configuration settings. You may also see other files and directories beginning with .. These are usually files and directories that are used to configure different programs on your computer. The prefix . is used to prevent these configuration files from cluttering the terminal when a standard ls command is used.

These three commands are the basic commands for navigating the filesystem on your computer: pwd, ls, and cd. Let’s explore some variations on those commands. What happens if you type cd on its own, without giving a directory?

$ cd

How can you check what happened? pwd gives us the answer!

$ pwd

/Users/nelle

It turns out that cd without an argument will return you to your home directory, which is great if you’ve got lost in your own filesystem.

Let’s try returning to the exercise-data directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to exercise-data in one step:

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

Check that we’ve moved to the right place by running pwd and ls -F.

If we want to move up one level from the data directory, we could use cd ... But there is another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been using relative paths. When you use a relative path with a command like ls or cd, it tries to find that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path from the root directory, which is indicated by a leading slash. The leading / tells the computer to follow the path from the root of the file system, so it always refers to exactly one directory, no matter where we are when we run the command.

This allows us to move to our shell-lesson-data directory from anywhere on the filesystem (including from inside exercise-data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to shell-lesson-data.

$ pwd

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

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

Run pwd and ls -F to ensure that we’re in the directory we expect.

Two More Shortcuts

The shell interprets a tilde (~) character at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in, which is faster than having to remember, then type, the full path. This is a very efficient way of moving back and forth between two directories – i.e. if you execute cd - twice, you end up back in the starting directory.

The difference between cd .. and cd - is that the former brings you up, while the latter brings you back.

Try it! First navigate to ~/Desktop/shell-lesson-data (you should already be there).
$ cd ~/Desktop/shell-lesson-data
Then cd into the exercise-data/creatures directory
$ cd exercise-data/creatures
Now if you run
$ cd -
you’ll see you’re back in ~/Desktop/shell-lesson-data. Run cd - again and you’re back in ~/Desktop/shell-lesson-data/exercise-data/creatures

Absolute vs Relative Paths

Starting from /Users/amanda/data, which of the following commands could Amanda use to navigate to her home directory, which is /Users/amanda?

cd .

cd /

cd /home/amanda

cd ../..

cd ~

cd home

cd ~/data/..

cd

cd ..

Solution

No: . stands for the current directory.

No: / stands for the root directory.

No: Amanda’s home directory is /Users/amanda.

No: this command goes up two levels, i.e. ends in /Users.

Yes: ~ stands for the user’s home directory, in this case /Users/amanda.

No: this command would navigate into a directory home in the current directory if it exists.

Yes: unnecessarily complicated, but correct.

Yes: shortcut to go back to the user’s home directory.

Yes: goes up one level.

Relative Path Resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls -F ../backup display?

../backup: No such file or directory

2012-12-01 2013-01-08 2013-01-27

2012-12-01/ 2013-01-08/ 2013-01-27/

original/ pnas_final/ pnas_sub/

Solution

No: there is a directory backup in /Users.

No: this is the content of Users/thing/backup, but with .., we asked for one level further up.

No: see previous explanation.

Yes: ../backup/ refers to /Users/backup/.

ls Reading Comprehension

Using the filesystem diagram below, if pwd displays /Users/backup, and -r tells ls to display things in reverse order, what command(s) will result in the following output:
pnas_sub/ pnas_final/ original/
ls pwd

ls -r -F

ls -r -F /Users/backup

Solution

No: pwd is not the name of a directory.

Yes: ls without directory argument lists files and directories in the current directory.

Yes: uses the absolute path explicitly.

General Syntax of a Shell Command

We have now encountered commands, options, and arguments, but it is perhaps useful to formalise some terminology.

Consider the command below as a general example of a command, which we will dissect into its component parts:

$ ls -F /

General syntax of a shell command

ls is the command, with an option -F and an argument /. We’ve already encountered options which either start with a single dash (-) or two dashes (--), and they change the behavior of a command. Arguments tell the command what to operate on (e.g. files and directories). Sometimes options and arguments are referred to as parameters. A command can be called with more than one option and more than one argument, but a command doesn’t always require an argument or an option.

You might sometimes see options being referred to as switches or flags, especially for options that take no argument. In this lesson we will stick with using the term option.

Each part is separated by spaces: if you omit the space between ls and -F the shell will look for a command called ls-F, which doesn’t exist. Also, capitalization is important. For example, ls -s will display the size of files and directories alongside the names, while ls -S will sort the files and directories by size, as shown below:

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

total 28
 4 animal-counts   4 creatures  12 numbers.txt   4 proteins   4 writing

Note that the sizes returned by ls -s are in blocks. As these are defined differently for different operating systems, you may not obtain the same figures as in the example.

$ ls -S exercise-data

animal-counts  creatures  proteins  writing  numbers.txt

Putting all that together, our command above gives us a listing of files and directories in the root directory /. An example of the output you might get from the above command is given below:

$ ls -F /

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

Nelle’s Pipeline: Organizing Files

Knowing this much about files and directories, Nelle is ready to organize the files that the protein assay machine will create.

She creates a directory called north-pacific-gyre (to remind herself where the data came from), which will contain the data files from the assay machine, and her data processing scripts.

Each of her physical samples is labelled according to her lab’s convention with a unique ten-character ID, such as ‘NENE01729A’. This ID is what she used in her collection log to record the location, time, depth, and other characteristics of the sample, so she decides to use it as part of each data file’s name. Since the assay machine’s output is plain text, she will call her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same directory.

Now in her current directory shell-lesson-data, Nelle can see what files she has using the command:

$ ls north-pacific-gyre/

This command is a lot to type, but she can let the shell do most of the work through what is called tab completion. If she types:

$ ls nor

and then presses Tab (the tab key on her keyboard), the shell automatically completes the directory name for her:

$ ls north-pacific-gyre/

Pressing Tab again does nothing, since there are multiple possibilities; pressing Tab twice brings up a list of all the files.

If Nelle adds G and presses Tab again, the shell will append ‘goo’ since all files that start with ‘g’ share the first three characters ‘goo’.

$ ls north-pacific-gyre/goo

To see all of those files, she can press Tab twice more.

ls north-pacific-gyre/goo
goodiff.sh   goostats.sh

This is called tab completion, and we will see it in many other tools as we go on.

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’.

BREAK

Overview

Teaching: 15 min
Exercises: 0 min

Questions

🥤 Coffee or 🫖 Tea?

Objectives

Make sure we are not too overloaded

Key Points

Working With Files and Directories

Overview

Teaching: 25 min
Exercises: 20 min

Questions

How can I create, copy, and delete files and directories?

How can I edit files?

Objectives

Create a directory hierarchy that matches a given diagram.

Create files in that hierarchy using an editor or by copying and renaming existing files.

Delete, copy and move specified files and/or directories.

Creating directories

We now know how to explore files and directories, but how do we create them in the first place?

In this episode we will learn about creating and moving files and directories, using the exercise-data/writing directory as an example.

Step one: see where we are and what we already have

We should still be in the shell-lesson-data directory on the Desktop, which we can check using:

$ pwd

/Users/nelle/Desktop/shell-lesson-data

Next we’ll move to the exercise-data/writing directory and see what it contains:

$ cd exercise-data/writing/

$ ls -F

haiku.txt  LittleWomen.txt

Create a directory

Let’s create a new directory called thesis using the command mkdir thesis (which has no output):

$ mkdir thesis

As you might guess from its name, mkdir means ‘make directory’. Since thesis is a relative path (i.e., does not have a leading slash, like /what/ever/thesis), the new directory is created in the current working directory:

$ ls -F

haiku.txt  LittleWomen.txt  thesis/

Since we’ve just created the thesis directory, there’s nothing in it yet:

$ ls -F thesis

Note that mkdir is not limited to creating single directories one at a time: you can use more than one directory argument. Also, the -p option (or --parents) allows mkdir to create a directory with nested subdirectories in a single operation. Putting these together, we can do:

$ mkdir -p ../project/data ../project/results

Both ../project/data and ../project/results are created, and also ../project is created automatically if needed because we used the -p option.

The -R option to the ls command will list all nested subdirectories within a directory. Let’s use ls -FR to recursively list the new directory hierarchy we just created in the project directory:

$ ls -FR ../project

../project/:
data/  results/

../project/data:

../project/results:

Two ways of doing the same thing

Using the shell to create a directory is no different than using a file explorer. If you open the current directory using your operating system’s graphical file explorer, the thesis directory will appear there too. While the shell and the file explorer are two different ways of interacting with the files, the files and directories themselves are the same.

Good names for files and directories

Complicated names of files and directories can make your life painful when working on the command line. Here we provide a few useful tips for the names of your files and directories.

Don’t use spaces.

Spaces can make a name more meaningful, but since spaces are used to separate arguments on the command line it is better to avoid them in names of files and directories. You can use - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/). To test this out, try typing mkdir north pacific gyreand see what directory (or directories!) are made when you check with ls -F.

Don’t begin the name with - (dash).

Commands treat names starting with - as options.

Stick with letters, numbers, . (period or ‘full stop’), - (dash) and _ (underscore).

Many other characters have special meanings on the command line. We will learn about some of these during this lesson. There are special characters that can cause your command to not work as expected and can even result in data loss.

If you need to refer to names of files or directories that have spaces or other special characters, you should surround the name in quotes ('').

Create a text file

Let’s change our working directory to thesis using cd, then run a text editor called Nano to create a file called draft.txt:

$ cd thesis
$ nano draft.txt

Which Editor?

When we say, ‘nano is a text editor’ we really do mean ‘text’: it can only work with plain character data, not tables, images, or any other human-friendly media. We use it in examples because it is one of the least complex text editors. However, because of this trait, it may not be powerful enough or flexible enough for the work you need to do after this workshop. On Unix systems (such as Linux and macOS), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit. On Windows, you may wish to use Notepad++. Windows also has a built-in editor called notepad that can be run from the command line in the same way as nano for the purposes of this lesson.

No matter what editor you use, you will need to know where it searches for and saves files. If you start it from the shell, it will (probably) use your current working directory as its default location. If you use your computer’s start menu, it may want to save files in your desktop or documents directory instead. You can change this by navigating to another directory the first time you ‘Save As…’

Let’s type in a few lines of text. Once we’re happy with our text, we can press Ctrl+O (press the Ctrl or Control key and, while holding it down, press the O key) to write our data to disk (we’ll be asked what file we want to save this to: press Return to accept the suggested default of draft.txt).

screenshot of nano text editor in action

Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.

Control, Ctrl, or ^ Key

The Control key is also called the ‘Ctrl’ key. There are various ways in which using the Control key may be described. For example, you may see an instruction to press the Control key and, while holding it down, press the X key, described as any of:

Control-X

Control+X

Ctrl-X

Ctrl+X

^X

C-x

In nano, along the bottom of the screen you’ll see ^G Get Help ^O WriteOut. This means that you can use Control-G to get help and Control-O to save your file.

Meta Key

The help that you obtain using Control-G includes a full list of keyboard shortcuts, of which the ones at the bottom of the screen are only a small selection. Many of these use the control key, as in the above examples, but there are some that are shown using M- (for “meta”) e.g. M-/ to go to the last line of the file. Typically this means that you would press Esc, then release it and press the other key, e.g. Esc /, although depending on your setup, it might work if instead you press the other key while holding down Alt.

nano doesn’t leave any output on the screen after it exits, but ls now shows that we have created a file called draft.txt:

$ ls

draft.txt

Creating Files a Different Way

We have seen how to create text files using the nano editor. Now, try the following command:
$ touch my_file.txt
What did the touch command do? When you look at your current directory using the GUI file explorer, does the file show up?

Use ls -l to inspect the files. How large is my_file.txt?

When might you want to create a file this way?

Solution

The touch command generates a new file called my_file.txt in your current directory. You can observe this newly generated file by typing ls at the command line prompt. my_file.txt can also be viewed in your GUI file explorer.

When you inspect the file with ls -l, note that the size of my_file.txt is 0 bytes. In other words, it contains no data. If you open my_file.txt using your text editor it is blank.

Some programs do not generate output files themselves, but instead require that empty files have already been generated. When the program is run, it searches for an existing file to populate with its output. The touch command allows you to efficiently generate a blank text file to be used by such programs.

What’s In A Name?

You may have noticed that all of Nelle’s files are named ‘something dot something’, and in this part of the lesson, we always used the extension .txt. This is just a convention: we can call a file mythesis or almost anything else we want. However, most people use two-part names most of the time to help them (and their programs) tell different kinds of files apart. The second part of such a name is called the filename extension and indicates what type of data the file holds: .txt signals a plain text file, .pdf indicates a PDF document, .cfg is a configuration file full of parameters for some program or other, .png is a PNG image, and so on.

This is just a convention, albeit an important one. Files contain bytes: it’s up to us and our programs to interpret those bytes according to the rules for plain text files, PDF documents, configuration files, images, and so on.

Naming a PNG image of a whale as whale.mp3 doesn’t somehow magically turn it into a recording of whale song, though it might cause the operating system to try to open it with a music player when someone double-clicks it.

Moving files and directories

Returning to the shell-lesson-data/exercise-data/writing directory,

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

In our thesis directory we have a file draft.txt which isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for ‘move’:

$ mv thesis/draft.txt thesis/quotes.txt

The first argument tells mv what we’re ‘moving’, while the second is where it’s to go. In this case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as renaming the file. Sure enough, ls shows us that thesis now contains one file called quotes.txt:

$ ls thesis

quotes.txt

One must be careful when specifying the target file name, since mv will silently overwrite any existing file with the same name, which could lead to data loss. An additional option, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Note that mv also works on directories.

Let’s move quotes.txt into the current working directory. We use mv once again, but this time we’ll use just the name of a directory as the second argument to tell mv that we want to keep the filename but put the file somewhere new. (This is why the command is called ‘move’.) In this case, the directory name we use is the special directory name . that we mentioned earlier.

$ mv thesis/quotes.txt .

The effect is to move the file from the directory it was in to the current working directory. ls now shows us that thesis is empty:

$ ls thesis

Alternatively, we can confirm the file quotes.txt is no longer present in the thesis directory by explicitly trying to list it:

$ ls thesis/quotes.txt

ls: cannot access 'thesis/quotes.txt': No such file or directory

ls with a filename or directory as an argument only lists the requested file or directory. If the file given as the argument doesn’t exist, the shell returns an error as we saw above. We can use this to see that quotes.txt is now present in our current directory:

$ ls quotes.txt

quotes.txt

Moving Files to a new folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed in the raw folder.
$ ls -F
 analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed
Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)
$ mv sucrose.dat maltose.dat ____/____
Solution
$ mv sucrose.dat maltose.dat ../raw
Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers to the current directory.

Copying files and directories

The cp command works very much like mv, except it copies a file instead of moving it. We can check that it did the right thing using ls with two paths as arguments — like most Unix commands, ls can be given multiple paths at once:

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt

quotes.txt   thesis/quotations.txt

We can also copy a directory and all its contents by using the recursive option -r, e.g. to back up a directory:

$ cp -r thesis thesis_backup

We can check the result by listing the contents of both the thesis and thesis_backup directory:

$ ls thesis thesis_backup

thesis:
quotations.txt

thesis_backup:
quotations.txt

Renaming Files

Suppose that you created a plain-text file in your current directory to contain a list of the statistical tests you will need to do to analyze your data, and named it: statstics.txt

After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so?

cp statstics.txt statistics.txt

mv statstics.txt statistics.txt

mv statstics.txt .

cp statstics.txt .

Solution

No. While this would create a file with the correct name, the incorrectly named file still exists in the directory and would need to be deleted.

Yes, this would work to rename the file.

No, the period(.) indicates where to move the file, but does not provide a new file name; identical file names cannot be created.

No, the period(.) indicates where to copy the file, but does not provide a new file name; identical file names cannot be created.

Moving and Copying

What is the output of the closing ls command in the sequence shown below?
$ pwd
/Users/jamie/data
$ ls
proteins.dat
$ mkdir recombined
$ mv proteins.dat recombined/
$ cp recombined/proteins.dat ../proteins-saved.dat
$ ls
proteins-saved.dat recombined

recombined

proteins.dat recombined

proteins-saved.dat

Solution

We start in the /Users/jamie/data directory, and create a new folder called recombined. The second line moves (mv) the file proteins.dat to the new folder (recombined). The third line makes a copy of the file we just moved. The tricky part here is where the file was copied to. Recall that .. means ‘go up a level’, so the copied file is now in /Users/jamie. Notice that .. is interpreted with respect to the current working directory, not with respect to the location of the file being copied. So, the only thing that will show using ls (in /Users/jamie/data) is the recombined folder.

No, see explanation above. proteins-saved.dat is located at /Users/jamie

Yes

No, see explanation above. proteins.dat is located at /Users/jamie/data/recombined

No, see explanation above. proteins-saved.dat is located at /Users/jamie

Removing files and directories

Returning to the shell-lesson-data/exercise-data/writing directory, let’s tidy up this directory by removing the quotes.txt file we created. The Unix command we’ll use for this is rm (short for ‘remove’):

$ rm quotes.txt

We can confirm the file has gone using ls:

$ ls quotes.txt

ls: cannot access 'quotes.txt': No such file or directory

Deleting Is Forever

The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most graphical interfaces to Unix do). Instead, when we delete files, they are unlinked from the file system so that their storage space on disk can be recycled. Tools for finding and recovering deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.

Using rm Safely

What happens when we execute rm -i thesis_backup/quotations.txt? Why would we want this protection when using rm?
Solution
rm: remove regular file 'thesis_backup/quotations.txt'? y
The -i option will prompt before (every) removal (use Y to confirm deletion or N to keep the file). The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By using the -i option, we have the chance to check that we are deleting only the files that we want to remove.

If we try to remove the thesis directory using rm thesis, we get an error message:

$ rm thesis

rm: cannot remove `thesis': Is a directory

This happens because rm by default only works on files, not directories.

rm can remove a directory and all its contents if we use the recursive option -r, and it will do so without any confirmation prompts:

$ rm -r thesis

Given that there is no way to retrieve files deleted using the shell, rm -r should be used with great caution (you might consider adding the interactive option rm -r -i).

Operations with multiple files and directories

Oftentimes one needs to copy or move several files at once. This can be done by providing a list of individual filenames, or specifying a naming pattern using wildcards.

Copy with Multiple Filenames

For this exercise, you can test the commands in the shell-lesson-data/exercise-data directory.

In the example below, what does cp do when given several filenames and a directory name?
$ mkdir backup
$ cp creatures/minotaur.dat creatures/unicorn.dat backup/
In the example below, what does cp do when given three or more file names?
$ cd creatures
$ ls -F
basilisk.dat  minotaur.dat  unicorn.dat
$ cp minotaur.dat unicorn.dat basilisk.dat
Solution

If given more than one file name followed by a directory name (i.e. the destination directory must be the last argument), cp copies the files to the named directory.

If given three file names, cp throws an error such as the one below, because it is expecting a directory name as the last argument.
cp: target 'basilisk.dat' is not a directory

Using wildcards for accessing multiple files at once

Wildcards

* is a wildcard, which matches zero or more characters. Let’s consider the shell-lesson-data/exercise-data/proteins directory: *.pdb matches ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only matches pentane.pdb and propane.pdb, because the ‘p’ at the front only matches filenames that begin with the letter ‘p’.

? is also a wildcard, but it matches exactly one character. So ?ethane.pdb would match methane.pdb whereas *ethane.pdb matches both ethane.pdb, and methane.pdb.

Wildcards can be used in combination with each other e.g. ???ane.pdb matches three characters followed by ane.pdb, giving cubane.pdb ethane.pdb octane.pdb.

When the shell sees a wildcard, it expands the wildcard to create a list of matching filenames before running the command that was asked for. As an exception, if a wildcard expression does not match any file, Bash will pass the expression as an argument to the command as it is. For example, typing ls *.pdf in the proteins directory (which contains only files with names ending with .pdb) results in an error message that there is no file called *.pdf. However, generally commands like wc and ls see the lists of file names matching these expressions, but not the wildcards themselves. It is the shell, not the other programs, that deals with expanding wildcards.

List filenames matching a pattern

When run in the proteins directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

ls *t*ane.pdb

ls *t?ne.*

ls *t??ne.pdb

ls ethane.*

Solution

The solution is 3.

1. shows all files whose names contain zero or more characters (*) followed by the letter t, then zero or more characters (*) followed by ane.pdb. This gives ethane.pdb methane.pdb octane.pdb pentane.pdb.

2. shows all files whose names start with zero or more characters (*) followed by the letter t, then a single character (?), then ne. followed by zero or more characters (*). This will give us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the solution.

4. only shows files starting with ethane..

More on Wildcards

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   └── datasets
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    └── all_november_files

Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:

$ cp *dataset* backup/datasets
$ cp ____calibration____ backup/calibration
$ cp 2015-____-____ send_to_bob/all_november_files/
$ cp ____ send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the blanks.

The resulting directory structure should look like this

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│   ├── calibration
│   │   ├── 2015-10-23-calibration.txt
│   │   ├── 2015-10-26-calibration.txt
│   │   └── 2015-11-23-calibration.txt
│   └── datasets
│       ├── 2015-10-23-dataset1.txt
│       ├── 2015-10-23-dataset2.txt
│       ├── 2015-10-23-dataset_overview.txt
│       ├── 2015-10-26-dataset1.txt
│       ├── 2015-10-26-dataset2.txt
│       ├── 2015-10-26-dataset_overview.txt
│       ├── 2015-11-23-dataset1.txt
│       ├── 2015-11-23-dataset2.txt
│       └── 2015-11-23-dataset_overview.txt
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    │   ├── 2015-10-23-dataset1.txt
    │   ├── 2015-10-23-dataset2.txt
    │   ├── 2015-10-23-dataset_overview.txt
    │   ├── 2015-11-23-dataset1.txt
    │   ├── 2015-11-23-dataset2.txt
    │   └── 2015-11-23-dataset_overview.txt
    └── all_november_files
        ├── 2015-11-23-calibration.txt
        ├── 2015-11-23-dataset1.txt
        ├── 2015-11-23-dataset2.txt
        └── 2015-11-23-dataset_overview.txt

Solution

$ cp *calibration.txt backup/calibration
$ cp 2015-11-* send_to_bob/all_november_files/
$ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/

Organizing Directories and Files

Jamie is working on a project and she sees that her files aren’t very well organized:
$ ls -F
analyzed/  fructose.dat    raw/   sucrose.dat
The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?
$ ls -F
analyzed/   raw/
$ ls analyzed
fructose.dat    sucrose.dat
Solution
mv *.dat analyzed
Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the ‘analyzed’ directory.

Reproduce a folder structure

You’re starting a new experiment and would like to duplicate the directory structure from your previous experiment so you can add new data.

Assume that the previous experiment is in a folder called 2016-05-18, which contains a data folder that in turn contains folders named raw and processed that contain data files. The goal is to copy the folder structure of the 2016-05-18 folder into a folder called 2016-05-20 so that your final directory structure looks like this:
2016-05-20/
└── data
   ├── processed
   └── raw
Which of the following set of commands would achieve this objective? What would the other commands do?
$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ cd data
$ mkdir raw processed
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed
$ mkdir -p 2016-05-20/data/raw
$ mkdir -p 2016-05-20/data/processed
$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ mkdir raw processed
Solution

The first two sets of commands achieve this objective. The first set uses relative paths to create the top-level directory before the subdirectories.

The third set of commands will give an error because the default behavior of mkdir won’t create a subdirectory of a non-existent directory: the intermediate level folders must be created first.

The fourth set of commands achieve this objective. Remember, the -p option, followed by a path of one or more directories, will cause mkdir to create any intermediate subdirectories as required.

The final set of commands generates the ‘raw’ and ‘processed’ directories at the same level as the ‘data’ directory.

I’m a terminal based editor get me out of here!

Some other editors use the terminal window, like nano, however they are not always as helpful in telling you how to use them. This can mean you accidentilly get stuck in the editor!
The default editor used by some commands means you need to know how to get out of them sometimes. If you are not used to them you can get stuck.

Emacs – get out with ^X ^C (maybe need ^G^X^C)

Vi – get out by pressing the esc, then :, then q! enter.

Pattern matching: globs

Unix shells recognises various wildcards in filenames. We have seen these two:

* matches any number of characters

? matches one character

These filename matching patterns, known as “globs”, are replaced with a list of matching filenames before the command is executed.
$ ls
1  3  4  5  a  a1  b  b1  c  c1  d  d1
$ ls *1
1  a1  b1  c1  d1
$ ls ??
a1  b1  c1  d1
Here is another glob for you […] matches any of the characters listed (or range of characters, e.g. [0-9])
$ ls [a-c]*
a  a1  b  b1  c  c1
And another glob {fred, barny, wilma} matches any of the comma separated names listed. For example ls *.{jpg,png} will list all your jpg and png files.

Use glob matching in acsoe/freetex-98/jungfrau Make a for loop that word counts only files from that date range

Key Points

cp [old] [new] copies a file.

mkdir [path] creates a new directory.

mv [old] [new] moves (renames) a file or directory.

rm [path] removes (deletes) a file.

* matches zero or more characters in a filename, so *.txt matches all files ending in .txt.

? matches any single character in a filename, so ?.txt matches a.txt but not any.txt.

Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.

The shell does not have a trash bin: once something is deleted, it’s really gone.

Most files’ names are something.extension. The extension isn’t required, and doesn’t guarantee anything, but is normally used to indicate the type of data in the file.

Depending on the type of work you do, you may need a more powerful text editor than Nano.

Pipes and Filters

Overview

Teaching: 25 min
Exercises: 10 min

Questions

How can I combine existing commands to do new things?

Objectives

Redirect a command’s output to a file.

Construct command pipelines with two or more stages.

Explain what usually happens if a program or pipeline isn’t given any input to process.

Explain the advantage of linking commands with pipes and filters.

Now that we know a few basic commands, we can finally look at the shell’s most powerful feature: the ease with which it lets us combine existing programs in new ways. We’ll start with the directory shell-lesson-data/exercise-data/proteins that contains six files describing some simple organic molecules. The .pdb extension indicates that these files are in Protein Data Bank format, a simple text format that specifies the type and position of each atom in the molecule.

$ ls proteins

cubane.pdb    methane.pdb    pentane.pdb
ethane.pdb    octane.pdb     propane.pdb

Let’s go into that directory with cd and run an example command wc cubane.pdb:

$ cd proteins
$ wc cubane.pdb

20  156 1158 cubane.pdb

wc is the ‘word count’ command: it counts the number of lines, words, and bytes in files (from left to right, in that order).

If we run the command wc *.pdb, the * in *.pdb matches zero or more characters, so the shell turns *.pdb into a list of all .pdb files in the current directory:

$ wc *.pdb

156  1158  cubane.pdb
84   622   ethane.pdb
57   422   methane.pdb
246  1828  octane.pdb
165  1226  pentane.pdb
111  825   propane.pdb
819  6081  total

Note that wc *.pdb also shows the total number of all lines in the last line of the output.

If we run wc -l instead of just wc, the output shows only the number of lines per file:

$ wc -l *.pdb

cubane.pdb
ethane.pdb
methane.pdb
octane.pdb
pentane.pdb
propane.pdb
total

The -c and -w options can also be used with the wc command, to show only the number of bytes or the number of words in the files.

Why Isn’t It Doing Anything?

What happens if a command is supposed to process a file, but we don’t give it a filename? For example, what if we type:
$ wc -l
but don’t type *.pdb (or anything else) after the command? Since it doesn’t have any filenames, wc assumes it is supposed to process input given at the command prompt, so it just sits there and waits for us to give it some data interactively. From the outside, though, all we see is it sitting there: the command doesn’t appear to do anything.

If you make this kind of mistake, you can escape out of this state by holding down the control key (Ctrl) and typing the letter C once and letting go of the Ctrl key. Ctrl+C

Capturing output from commands

Which of these files contains the fewest lines? It’s an easy question to answer when there are only six files, but what if there were 6000? Our first step toward a solution is to run the command:

$ wc -l *.pdb > lengths.txt

The greater than symbol, >, tells the shell to redirect the command’s output to a file instead of printing it to the screen. (This is why there is no screen output: everything that wc would have printed has gone into the file lengths.txt instead.) The shell will create the file if it doesn’t exist. If the file exists, it will be silently overwritten, which may lead to data loss and thus requires some caution. ls lengths.txt confirms that the file exists:

$ ls lengths.txt

lengths.txt

We can now send the content of lengths.txt to the screen using cat lengths.txt. The cat command gets its name from ‘concatenate’ i.e. join together, and it prints the contents of files one after another. There’s only one file in this case, so cat just shows us what it contains:

$ cat lengths.txt

cubane.pdb
ethane.pdb
methane.pdb
octane.pdb
pentane.pdb
propane.pdb
total

Output Page by Page

We’ll continue to use cat in this lesson, for convenience and consistency, but it has the disadvantage that it always dumps the whole file onto your screen. More useful in practice is the command less, which you use with less lengths.txt. This displays a screenful of the file, and then stops. You can go forward one screenful by pressing the spacebar, or back one by pressing b. Press q to quit.

Filtering output

Next we’ll use the sort command to sort the contents of the lengths.txt file. But first we’ll use an exercise to learn a little about the sort command:

What Does sort -n Do?

The file shell-lesson-data/exercise-data/numbers.txt contains the following lines:
10
2
19
22
6
If we run sort on this file, the output is:
10
19
2
22
6
If we run sort -n on the same file, we get this instead:
2
6
10
19
22
Explain why -n has this effect.

Solution

The -n option specifies a numerical rather than an alphanumerical sort.

We will also use the -n option to specify that the sort is numerical instead of alphanumerical. This does not change the file; instead, it sends the sorted result to the screen:

$ sort -n lengths.txt

methane.pdb
ethane.pdb
propane.pdb
cubane.pdb
pentane.pdb
octane.pdb
total

We can put the sorted list of lines in another temporary file called sorted-lengths.txt by putting > sorted-lengths.txt after the command, just as we used > lengths.txt to put the output of wc into lengths.txt. Once we’ve done that, we can run another command called head to get the first few lines in sorted-lengths.txt:

$ sort -n lengths.txt > sorted-lengths.txt
$ head -n 1 sorted-lengths.txt

  9  methane.pdb

Using -n 1 with head tells it that we only want the first line of the file; -n 20 would get the first 20, and so on. Since sorted-lengths.txt contains the lengths of our files ordered from least to greatest, the output of head must be the file with the fewest lines.

Redirecting to the same file

It’s a very bad idea to try redirecting the output of a command that operates on a file to the same file. For example:
$ sort -n lengths.txt > lengths.txt
Doing something like this may give you incorrect results and/or delete the contents of lengths.txt.

What Does >> Mean?

We have seen the use of >, but there is a similar operator >> which works slightly differently. We’ll learn about the differences between these two operators by printing some strings. We can use the echo command to print strings e.g.
$ echo The echo command prints text
The echo command prints text
Now test the commands below to reveal the difference between the two operators:
$ echo hello > testfile01.txt
and:
$ echo hello >> testfile02.txt
Hint: Try executing each command twice in a row and then examining the output files.

Solution

In the first example with >, the string ‘hello’ is written to testfile01.txt, but the file gets overwritten each time we run the command.

We see from the second example that the >> operator also writes ‘hello’ to a file (in this casetestfile02.txt), but appends the string to the file if it already exists (i.e. when we run it for the second time).

Appending Data

We have already met the head command, which prints lines from the start of a file. tail is similar, but prints lines from the end of a file instead.

Consider the file shell-lesson-data/exercise-data/animal-counts/animals.csv. After these commands, select the answer that corresponds to the file animals-subset.csv:
$ head -n 3 animals.csv > animals-subset.csv
$ tail -n 2 animals.csv >> animals-subset.csv
The first three lines of animals.csv

The last two lines of animals.csv

The first three lines and the last two lines of animals.csv

The second and third lines of animals.csv

Solution

Option 3 is correct. For option 1 to be correct we would only run the head command. For option 2 to be correct we would only run the tail command. For option 4 to be correct we would have to pipe the output of head into tail -n 2 by doing head -n 3 animals.csv | tail -n 2 > animals-subset.csv

Passing output to another command

In our example of finding the file with the fewest lines, we are using two intermediate files lengths.txt and sorted-lengths.txt to store output. This is a confusing way to work because even once you understand what wc, sort, and head do, those intermediate files make it hard to follow what’s going on. We can make it easier to understand by running sort and head together:

$ sort -n lengths.txt | head -n 1

  9  methane.pdb

The vertical bar, |, between the two commands is called a pipe. It tells the shell that we want to use the output of the command on the left as the input to the command on the right.

This has removed the need for the sorted-lengths.txt file.

Combining multiple commands

Nothing prevents us from chaining pipes consecutively. We can for example send the output of wc directly to sort, and then the resulting output to head. This removes the need for any intermediate files.

We’ll start by using a pipe to send the output of wc to sort:

$ wc -l *.pdb | sort -n

methane.pdb
ethane.pdb
propane.pdb
cubane.pdb
pentane.pdb
octane.pdb
total

We can then send that output through another pipe, to head, so that the full pipeline becomes:

$ wc -l *.pdb | sort -n | head -n 1

   9  methane.pdb

This is exactly like a mathematician nesting functions like log(3x) and saying ‘the log of three times x’. In our case, the calculation is ‘head of sort of line count of *.pdb’.

The redirection and pipes used in the last few commands are illustrated below:

Piping Commands Together

In our current directory, we want to find the 3 files which have the least number of lines. Which command listed below would work?

wc -l * > sort -n > head -n 3

wc -l * | sort -n | head -n 1-3

wc -l * | head -n 3 | sort -n

wc -l * | sort -n | head -n 3

Solution

Option 4 is the solution. The pipe character | is used to connect the output from one command to the input of another. > is used to redirect standard output to a file. Try it in the shell-lesson-data/exercise-data/proteins directory!

Tools designed to work together

This idea of linking programs together is why Unix has been so successful. Instead of creating enormous programs that try to do many different things, Unix programmers focus on creating lots of simple tools that each do one job well, and that work well with each other. This programming model is called ‘pipes and filters’. We’ve already seen pipes; a filter is a program like wc or sort that transforms a stream of input into a stream of output. Almost all of the standard Unix tools can work this way: unless told to do otherwise, they read from standard input, do something with what they’ve read, and write to standard output.

The key is that any program that reads lines of text from standard input and writes lines of text to standard output can be combined with every other program that behaves this way as well. You can and should write your programs this way so that you and other people can put those programs into pipes to multiply their power.

Pipe Reading Comprehension

A file called animals.csv (in the shell-lesson-data/exercise-data/animal-counts folder) contains the following data:
2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-06,fox,4
2012-11-07,rabbit,16
2012-11-07,bear,1
What text passes through each of the pipes and the final redirect in the pipeline below? Note, the sort -r command sorts in reverse order.
$ cat animals.csv | head -n 5 | tail -n 3 | sort -r > final.txt
Hint: build the pipeline up one command at a time to test your understanding
Solution

The head command extracts the first 5 lines from animals.csv. Then, the last 3 lines are extracted from the previous 5 by using the tail command. With the sort -r command those 3 lines are sorted in reverse order and finally, the output is redirected to a file final.txt. The content of this file can be checked by executing cat final.txt. The file should contain the following lines:
2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-05,raccoon,7

Pipe Construction

For the file animals.csv from the previous exercise, consider the following command:
$ cut -d , -f 2 animals.csv
The cut command is used to remove or ‘cut out’ certain sections of each line in the file, and cut expects the lines to be separated into columns by a Tab character. A character used in this way is a called a delimiter. In the example above we use the -d option to specify the comma as our delimiter character. We have also used the -f option to specify that we want to extract the second field (column). This gives the following output:
deer
rabbit
raccoon
rabbit
deer
fox
rabbit
bear
The uniq command filters out adjacent matching lines in a file. How could you extend this pipeline (using uniq and another command) to find out what animals the file contains (without any duplicates in their names)?
Solution
$ cut -d , -f 2 animals.csv | sort | uniq

Which Pipe?

The file animals.csv contains 8 lines of data formatted as follows:
2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
...
The uniq command has a -c option which gives a count of the number of times a line occurs in its input. Assuming your current directory is shell-lesson-data/exercise-data/animal-counts, what command would you use to produce a table that shows the total count of each type of animal in the file?

sort animals.csv | uniq -c

sort -t, -k2,2 animals.csv | uniq -c

cut -d , -f 2 animals.csv | uniq -c

cut -d , -f 2 animals.csv | sort | uniq -c

cut -d , -f 2 animals.csv | sort | uniq -c | wc -l

Solution

Option 4. is the correct answer. If you have difficulty understanding why, try running the commands, or sub-sections of the pipelines (make sure you are in the shell-lesson-data/exercise-data/animal-counts directory).

Nelle’s Pipeline: Checking Files

Nelle has run her samples through the assay machines and created 17 files in the north-pacific-gyre directory described earlier. As a quick check, starting from the shell-lesson-data directory, Nelle types:

$ cd north-pacific-gyre
$ wc -l *.txt

The output is 18 lines that look like this:

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
NENE01751A.txt
NENE01751B.txt
NENE01812A.txt
... ...

Now she types this:

$ wc -l *.txt | sort -n | head -n 5

NENE02018B.txt
NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
NENE01751A.txt

Whoops: one of the files is 60 lines shorter than the others. When she goes back and checks it, she sees that she did that assay at 8:00 on a Monday morning — someone was probably in using the machine on the weekend, and she forgot to reset it. Before re-running that sample, she checks to see if any files have too much data:

$ wc -l *.txt | sort -n | tail -n 5

NENE02040B.txt
NENE02040Z.txt
NENE02043A.txt
NENE02043B.txt
total

Those numbers look good — but what’s that ‘Z’ doing there in the third-to-last line? All of her samples should be marked ‘A’ or ‘B’; by convention, her lab uses ‘Z’ to indicate samples with missing information. To find others like it, she does this:

$ ls *Z.txt

NENE01971Z.txt    NENE02040Z.txt

Sure enough, when she checks the log on her laptop, there’s no depth recorded for either of those samples. Since it’s too late to get the information any other way, she must exclude those two files from her analysis. She could delete them using rm, but there are actually some analyses she might do later where depth doesn’t matter, so instead, she’ll have to be careful later on to select files using the wildcard expressions NENE*A.txt NENE*B.txt.

Removing Unneeded Files

Suppose you want to delete your processed data files, and only keep your raw files and processing script to save storage. The raw files end in .dat and the processed files end in .txt. Which of the following would remove all the processed data files, and only the processed data files?

rm ?.txt

rm *.txt

rm * .txt

rm *.*

Solution

This would remove .txt files with one-character names

This is correct answer

The shell would expand * to match everything in the current directory, so the command would try to remove all matched files and an additional file called .txt

The shell would expand *.* to match all files with any extension, so this command would delete all files

Key Points

wc counts lines, words, and bytes in its inputs.

cat displays the contents of its inputs.

sort sorts its inputs.

head displays the first 10 lines of its input.

tail displays the last 10 lines of its input.

command > [file] redirects a command’s output to a file (overwriting any existing content).

command >> [file] appends a command’s output to a file.

[first] | [second] is a pipeline: the output of the first command is used as the input to the second.

The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).

LUNCH

Overview

Teaching: 60 min
Exercises: 0 min

Questions

🥪 🍕 🍩 🫖 Hunt or Gather?

Objectives

Make sure we are not too overloaded

Eat stuff

Key Points

Loops

Overview

Teaching: 25 min
Exercises: 10 min

Questions

How can I perform the same actions on many different files?

Objectives

Write a loop that applies one or more commands separately to each file in a set of files.

Trace the values taken on by a loop variable during execution of the loop.

Explain the difference between a variable’s name and its value.

Explain why spaces and some punctuation characters shouldn’t be used in file names.

Demonstrate how to see what commands have recently been executed.

Re-run recently executed commands without retyping them.

Loops are a programming construct which allow us to repeat a command or set of commands for each item in a list. As such they are key to productivity improvements through automation. Similar to wildcards and tab completion, using loops also reduces the amount of typing required (and hence reduces the number of typing mistakes).

Suppose we have several hundred genome data files with names like basilisk.dat, minotaur.dat, and unicorn.dat. For this example, we’ll use the exercise-data/creatures directory which only has three example files, but the principles can be applied to many many more files at once.

The structure of these files is the same: the common name, classification, and updated date are presented on the first three lines, with DNA sequences on the following lines. Let’s look at the files:

$ head -n 5 basilisk.dat minotaur.dat unicorn.dat

We would like to print out the classification for each species, which is given on the second line of each file. For each file, we would need to execute the command head -n 2 and pipe this to tail -n 1. We’ll use a loop to solve this problem, but first let’s look at the general form of a loop:

for thing in list_of_things
do
    operation_using $thing    # Indentation within the loop is not required, but aids legibility
done

and we can apply this to our example like this:

$ for filename in basilisk.dat minotaur.dat unicorn.dat
> do
>     head -n 2 $filename | tail -n 1
> done

CLASSIFICATION: basiliscus vulgaris
CLASSIFICATION: bos hominus
CLASSIFICATION: equus monoceros

Follow the Prompt

The shell prompt changes from $ to > and back again as we were typing in our loop. The second prompt, >, is different to remind us that we haven’t finished typing a complete command yet. A semicolon, ;, can be used to separate two commands written on a single line.

When the shell sees the keyword for, it knows to repeat a command (or group of commands) once for each item in a list. Each time the loop runs (called an iteration), an item in the list is assigned in sequence to the variable, and the commands inside the loop are executed, before moving on to the next item in the list. Inside the loop, we call for the variable’s value by putting $ in front of it. The $ tells the shell interpreter to treat the variable as a variable name and substitute its value in its place, rather than treat it as text or an external command.

In this example, the list is three filenames: basilisk.dat, minotaur.dat, and unicorn.dat. Each time the loop iterates, it will assign a file name to the variable filename and run the head command. The first time through the loop, $filename is basilisk.dat. The interpreter runs the command head on basilisk.dat and pipes the first two lines to the tail command, which then prints the second line of basilisk.dat. For the second iteration, $filename becomes minotaur.dat. This time, the shell runs head on minotaur.dat and pipes the first two lines to the tail command, which then prints the second line of minotaur.dat. For the third iteration, $filename becomes unicorn.dat, so the shell runs the head command on that file, and tail on the output of that. Since the list was only three items, the shell exits the for loop.

Same Symbols, Different Meanings

Here we see > being used as a shell prompt, whereas > is also used to redirect output. Similarly, $ is used as a shell prompt, but, as we saw earlier, it is also used to ask the shell to get the value of a variable.

If the shell prints > or $ then it expects you to type something, and the symbol is a prompt.

If you type > or $ yourself, it is an instruction from you that the shell should redirect output or get the value of a variable.

When using variables it is also possible to put the names into curly braces to clearly delimit the variable name: $filename is equivalent to ${filename}, but is different from ${file}name. You may find this notation in other people’s programs.

We have called the variable in this loop filename in order to make its purpose clearer to human readers. The shell itself doesn’t care what the variable is called; if we wrote this loop as:

$ for x in basilisk.dat minotaur.dat unicorn.dat
> do
>     head -n 2 $x | tail -n 1
> done

or:

$ for temperature in basilisk.dat minotaur.dat unicorn.dat
> do
>     head -n 2 $temperature | tail -n 1
> done

it would work exactly the same way. Don’t do this. Programs are only useful if people can understand them, so meaningless names (like x) or misleading names (like temperature) increase the odds that the program won’t do what its readers think it does.

In the above examples, the variables (thing, filename, x and temperature) could have been given any other name, as long as it is meaningful to both the person writing the code and the person reading it.

Note also that loops can be used for other things than filenames, like a list of numbers or a subset of data.

Write your own loop

How would you write a loop that echoes all 10 numbers from 0 to 9?
Solution
$ for loop_variable in 0 1 2 3 4 5 6 7 8 9
> do
>     echo $loop_variable
> done
0
1
2
3
4
5
6
7
8
9

Variables in Loops

This exercise refers to the shell-lesson-data/exercise-data/proteins directory. ls *.pdb gives the following output:
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
What is the output of the following code?
$ for datafile in *.pdb
> do
>     ls *.pdb
> done
Now, what is the output of the following code?
$ for datafile in *.pdb
> do
>     ls $datafile
> done
Why do these two loops give different outputs?
Solution

The first code block gives the same output on each iteration through the loop. Bash expands the wildcard *.pdb within the loop body (as well as before the loop starts) to match all files ending in .pdb and then lists them using ls. The expanded loop would look like this:
$ for datafile in cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
> do
>     ls cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
> done
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
The second code block lists a different file on each loop iteration. The value of the datafile variable is evaluated using $datafile, and then listed using ls.
cubane.pdb
ethane.pdb
methane.pdb
octane.pdb
pentane.pdb
propane.pdb

Limiting Sets of Files

What would be the output of running the following loop in the shell-lesson-data/exercise-data/proteins directory?
$ for filename in c*
> do
>     ls $filename
> done
No files are listed.

All files are listed.

Only cubane.pdb, octane.pdb and pentane.pdb are listed.

Only cubane.pdb is listed.

Solution

4 is the correct answer. * matches zero or more characters, so any file name starting with the letter c, followed by zero or more other characters will be matched.

How would the output differ from using this command instead?
$ for filename in *c*
> do
>     ls $filename
> done
The same files would be listed.

All the files are listed this time.

No files are listed this time.

The files cubane.pdb and octane.pdb will be listed.

Only the file octane.pdb will be listed.

Solution

4 is the correct answer. * matches zero or more characters, so a file name with zero or more characters before a letter c and zero or more characters after the letter c will be matched.

Saving to a File in a Loop - Part One

In the shell-lesson-data/exercise-data/proteins directory, what is the effect of this loop?
for alkanes in *.pdb
do
    echo $alkanes
    cat $alkanes > alkanes.pdb
done
Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb, and the text from propane.pdb will be saved to a file called alkanes.pdb.

Prints cubane.pdb, ethane.pdb, and methane.pdb, and the text from all three files would be concatenated and saved to a file called alkanes.pdb.

Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, and pentane.pdb, and the text from propane.pdb will be saved to a file called alkanes.pdb.

None of the above.

Solution

The text from each file in turn gets written to the alkanes.pdb file. However, the file gets overwritten on each loop iteration, so the final content of alkanes.pdb is the text from the propane.pdb file.

Saving to a File in a Loop - Part Two

Also in the shell-lesson-data/exercise-data/proteins directory, what would be the output of the following loop?
for datafile in *.pdb
do
    cat $datafile >> all.pdb
done
All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, and pentane.pdb would be concatenated and saved to a file called all.pdb.

The text from ethane.pdb will be saved to a file called all.pdb.

All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb would be concatenated and saved to a file called all.pdb.

All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb would be printed to the screen and saved to a file called all.pdb.

Solution

3 is the correct answer. >> appends to a file, rather than overwriting it with the redirected output from a command. Given the output from the cat command has been redirected, nothing is printed to the screen.

If the all.pdb already existed before the loop was executed, then its original contents would remain at the start of the file. If this behaviour is not desirable, then adding rm -f all.pdb could be added at the start of the program, before the for loop. This would ensure that any existing all.pdb file is removed first.

Let’s continue with our example in the shell-lesson-data/exercise-data/creatures directory. Here’s a slightly more complicated loop:

$ for filename in *.dat
> do
>     echo $filename
>     head -n 100 $filename | tail -n 20
> done

The shell starts by expanding *.dat to create the list of files it will process. The loop body then executes two commands for each of those files. The first command, echo, prints its command-line arguments to standard output. For example:

$ echo hello there

prints:

hello there

In this case, since the shell expands $filename to be the name of a file, echo $filename prints the name of the file. Note that we can’t write this as:

$ for filename in *.dat
> do
>     $filename
>     head -n 100 $filename | tail -n 20
> done

because then the first time through the loop, when $filename expanded to basilisk.dat, the shell would try to run basilisk.dat as a program. Finally, the head and tail combination selects lines 81-100 from whatever file is being processed (assuming the file has at least 100 lines).

Spaces in Names

Spaces are used to separate the elements of the list that we are going to loop over. If one of those elements contains a space character, we need to surround it with quotes, and do the same thing to our loop variable. Suppose our data files are named:
red dragon.dat
purple unicorn.dat
To loop over these files, we would need to add double quotes like so:
$ for filename in "red dragon.dat" "purple unicorn.dat"
> do
>     head -n 100 "$filename" | tail -n 20
> done
It is simpler to avoid using spaces (or other special characters) in filenames.

The files above don’t exist, so if we run the above code, the head command will be unable to find them, however the error message returned will show the name of the files it is expecting:
head: cannot open ‘red dragon.dat’ for reading: No such file or directory
head: cannot open ‘purple unicorn.dat’ for reading: No such file or directory
Try removing the quotes around $filename in the loop above to see the effect of the quote marks on spaces. Note that we get a result from the loop command for unicorn.dat when we run this code in the creatures directory:
head: cannot open ‘red’ for reading: No such file or directory
head: cannot open ‘dragon.dat’ for reading: No such file or directory
head: cannot open ‘purple’ for reading: No such file or directory
CGGTACCGAA
AAGGGTCGCG
CAAGTGTTCC
...

We would like to modify each of the files in shell-lesson-data/exercise-data/creatures, but also save a version of the original files, naming the copies original-basilisk.dat and original-unicorn.dat. We can’t use:

$ cp *.dat original-*.dat

because that would expand to:

$ cp basilisk.dat minotaur.dat unicorn.dat original-*.dat

This wouldn’t back up our files, instead we get an error:

cp: target `original-*.dat' is not a directory

This problem arises when cp receives more than two inputs. When this happens, it expects the last input to be a directory where it can copy all the files it was passed. Since there is no directory named original-*.dat in the creatures directory we get an error.

Instead, we can use a loop:

$ for filename in *.dat
> do
>     cp $filename original-$filename
> done

This loop runs the cp command once for each filename. The first time, when $filename expands to basilisk.dat, the shell executes:

cp basilisk.dat original-basilisk.dat

The second time, the command is:

cp minotaur.dat original-minotaur.dat

The third and last time, the command is:

cp unicorn.dat original-unicorn.dat

Since the cp command does not normally produce any output, it’s hard to check that the loop is doing the correct thing. However, we learned earlier how to print strings using echo, and we can modify the loop to use echo to print our commands without actually executing them. As such we can check what commands would be run in the unmodified loop.

The following diagram shows what happens when the modified loop is executed, and demonstrates how the judicious use of echo is a good debugging technique.

Nelle’s Pipeline: Processing Files

Nelle is now ready to process her data files using goostats.sh — a shell script written by her supervisor. This calculates some statistics from a protein sample file, and takes two arguments:

an input file (containing the raw data)
an output file (to store the calculated statistics)

Since she’s still learning how to use the shell, she decides to build up the required commands in stages. Her first step is to make sure that she can select the right input files — remember, these are ones whose names end in ‘A’ or ‘B’, rather than ‘Z’. Starting from her home directory, Nelle types:

$ cd north-pacific-gyre
$ for datafile in NENE*A.txt NENE*B.txt
> do
>     echo $datafile
> done

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...
NENE02043A.txt
NENE02043B.txt

Her next step is to decide what to call the files that the goostats.sh analysis program will create. Prefixing each input file’s name with ‘stats’ seems simple, so she modifies her loop to do that:

$ for datafile in NENE*A.txt NENE*B.txt
> do
>     echo $datafile stats-$datafile
> done

NENE01729A.txt stats-NENE01729A.txt
NENE01729B.txt stats-NENE01729B.txt
NENE01736A.txt stats-NENE01736A.txt
...
NENE02043A.txt stats-NENE02043A.txt
NENE02043B.txt stats-NENE02043B.txt

She hasn’t actually run goostats.sh yet, but now she’s sure she can select the right files and generate the right output filenames.

Typing in commands over and over again is becoming tedious, though, and Nelle is worried about making mistakes, so instead of re-entering her loop, she presses ↑. In response, the shell redisplays the whole loop on one line (using semi-colons to separate the pieces):

$ for datafile in NENE*A.txt NENE*B.txt; do echo $datafile stats-$datafile; done

Using the left arrow key, Nelle backs up and changes the command echo to bash goostats.sh:

$ for datafile in NENE*A.txt NENE*B.txt; do bash goostats.sh $datafile stats-$datafile; done

When she presses Enter, the shell runs the modified command. However, nothing appears to happen — there is no output. After a moment, Nelle realizes that since her script doesn’t print anything to the screen any longer, she has no idea whether it is running, much less how quickly. She kills the running command by typing Ctrl+C, uses ↑ to repeat the command, and edits it to read:

$ for datafile in NENE*A.txt NENE*B.txt; do echo $datafile;
bash goostats.sh $datafile stats-$datafile; done

Beginning and End

We can move to the beginning of a line in the shell by typing Ctrl+A and to the end using Ctrl+E.

When she runs her program now, it produces one line of output every five seconds or so:

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...

1518 times 5 seconds, divided by 3600, tells her that her script will take about two hours to run. As a final check, she opens another terminal window, goes into north-pacific-gyre, and uses cat stats-NENE01729B.txt to examine one of the output files. It looks good, so she decides to get some coffee and catch up on her reading.

Those Who Know History Can Choose to Repeat It

Another way to repeat previous work is to use the history command to get a list of the last few hundred commands that have been executed, and then to use !123 (where ‘123’ is replaced by the command number) to repeat one of those commands. For example, if Nelle types this:
$ history | tail -n 5
  456  ls -l NENE0*.txt
  457  rm stats-NENE01729B.txt.txt
  458  bash goostats.sh NENE01729B.txt stats-NENE01729B.txt
  459  ls -l NENE0*.txt
  460  history
then she can re-run goostats.sh on NENE01729B.txt simply by typing !458.

Other History Commands

There are a number of other shortcut commands for getting at the history.

Ctrl+R enters a history search mode ‘reverse-i-search’ and finds the most recent command in your history that matches the text you enter next. Press Ctrl+R one or more additional times to search for earlier matches. You can then use the left and right arrow keys to choose that line and edit it then hit Return to run the command.

!! retrieves the immediately preceding command (you may or may not find this more convenient than using ↑)

!$ retrieves the last word of the last command. That’s useful more often than you might expect: after bash goostats.sh NENE01729B.txt stats-NENE01729B.txt, you can type less !$ to look at the file stats-NENE01729B.txt, which is quicker than doing ↑ and editing the command-line.

Doing a Dry Run

A loop is a way to do many things at once — or to make many mistakes at once if it does the wrong thing. One way to check what a loop would do is to echo the commands it would run instead of actually running them.

Suppose we want to preview the commands the following loop will execute without actually running those commands:
$ for datafile in *.pdb
> do
>     cat $datafile >> all.pdb
> done
What is the difference between the two loops below, and which one would we want to run?
# Version 1
$ for datafile in *.pdb
> do
>     echo cat $datafile >> all.pdb
> done
# Version 2
$ for datafile in *.pdb
> do
>     echo "cat $datafile >> all.pdb"
> done
Solution

The second version is the one we want to run. This prints to screen everything enclosed in the quote marks, expanding the loop variable name because we have prefixed it with a dollar sign. It also does not modify nor create the file all.pdb, as the >> is treated literally as part of a string rather than as a redirection instruction.

The first version appends the output from the command echo cat $datafile to the file, all.pdb. This file will just contain the list; cat cubane.pdb, cat ethane.pdb, cat methane.pdb etc.

Try both versions for yourself to see the output! Be sure to open the all.pdb file to view its contents. You may wish to delete all.pdb before trying version 2, to remove the output that was added by version 1.

Nested Loops

Suppose we want to set up a directory structure to organize some experiments measuring reaction rate constants with different compounds and different temperatures. What would be the result of the following code:
$ for species in cubane ethane methane
> do
>     for temperature in 25 30 37 40
>     do
>         mkdir $species-$temperature
>     done
> done
Solution

We have a nested loop, i.e. contained within another loop, so for each species in the outer loop, the inner loop (the nested loop) iterates over the list of temperatures, and creates a new directory for each combination.

Try running the code for yourself to see which directories are created!

Key Points

A for loop repeats commands once for every thing in a list.

Every for loop needs a variable to refer to the thing it is currently operating on.

Use $name to expand a variable (i.e., get its value). ${name} can also be used.

Do not use spaces, quotes, or wildcard characters such as ‘*’ or ‘?’ in filenames, as it complicates variable expansion.

Give files consistent names that are easy to match with wildcard patterns to make it easy to select them for looping.

Use the up-arrow key to scroll up through previous commands to edit and repeat them.

Use Ctrl+R to search through the previously entered commands.

Use history to display recent commands, and ![number] to repeat a command by number.

Shell Scripts

Overview

Teaching: 30 min
Exercises: 15 min

Questions

How can I save and re-use commands?

Objectives

Write a shell script that runs a command or series of commands for a fixed set of files.

Run a shell script from the command line.

Write a shell script that operates on a set of files defined by the user on the command line.

Create pipelines that include shell scripts you, and others, have written.

We are finally ready to see what makes the shell such a powerful programming environment. We are going to take the commands we repeat frequently and save them in files so that we can re-run all those operations again later by typing a single command. For historical reasons, a bunch of commands saved in a file is usually called a shell script, but make no mistake: these are actually small programs.

Not only will writing shell scripts make your work faster — you won’t have to retype the same commands over and over again — it will also make it more accurate (fewer chances for typos) and more reproducible. If you come back to your work later (or if someone else finds your work and wants to build on it) you will be able to reproduce the same results simply by running your script, rather than having to remember or retype a long list of commands.

Let’s start by going back to proteins/ and creating a new file, middle.sh which will become our shell script:

$ cd proteins
$ nano middle.sh

The command nano middle.sh opens the file middle.sh within the text editor ‘nano’ (which runs within the shell). If the file does not exist, it will be created. We can use the text editor to directly edit the file – we’ll simply insert the following line:

head -n 15 octane.pdb | tail -n 5

This is a variation on the pipe we constructed earlier: it selects lines 11-15 of the file octane.pdb. Remember, we are not running it as a command just yet: we are putting the commands in a file.

Then we save the file (Ctrl-O in nano), and exit the text editor (Ctrl-X in nano). Check that the directory proteins now contains a file called middle.sh.

Once we have saved the file, we can ask the shell to execute the commands it contains. Our shell is called bash, so we run the following command:

$ bash middle.sh

ATOM      9  H           1      -4.502   0.681   0.785  1.00  0.00
ATOM     10  H           1      -5.254  -0.243  -0.537  1.00  0.00
ATOM     11  H           1      -4.357   1.252  -0.895  1.00  0.00
ATOM     12  H           1      -3.009  -0.741  -1.467  1.00  0.00
ATOM     13  H           1      -3.172  -1.337   0.206  1.00  0.00

Sure enough, our script’s output is exactly what we would get if we ran that pipeline directly.

Text vs. Whatever

We usually call programs like Microsoft Word or LibreOffice Writer “text editors”, but we need to be a bit more careful when it comes to programming. By default, Microsoft Word uses .docx files to store not only text, but also formatting information about fonts, headings, and so on. This extra information isn’t stored as characters and doesn’t mean anything to tools like head: they expect input files to contain nothing but the letters, digits, and punctuation on a standard computer keyboard. When editing programs, therefore, you must either use a plain text editor, or be careful to save files as plain text.

What if we want to select lines from an arbitrary file? We could edit middle.sh each time to change the filename, but that would probably take longer than typing the command out again in the shell and executing it with a new file name. Instead, let’s edit middle.sh and make it more versatile:

$ nano middle.sh

Now, within “nano”, replace the text octane.pdb with the special variable called $1:

head -n 15 "$1" | tail -n 5

Inside a shell script, $1 means ‘the first filename (or other argument) on the command line’. We can now run our script like this:

$ bash middle.sh octane.pdb

ATOM      9  H           1      -4.502   0.681   0.785  1.00  0.00
ATOM     10  H           1      -5.254  -0.243  -0.537  1.00  0.00
ATOM     11  H           1      -4.357   1.252  -0.895  1.00  0.00
ATOM     12  H           1      -3.009  -0.741  -1.467  1.00  0.00
ATOM     13  H           1      -3.172  -1.337   0.206  1.00  0.00

or on a different file like this:

$ bash middle.sh pentane.pdb

ATOM      9  H           1       1.324   0.350  -1.332  1.00  0.00
ATOM     10  H           1       1.271   1.378   0.122  1.00  0.00
ATOM     11  H           1      -0.074  -0.384   1.288  1.00  0.00
ATOM     12  H           1      -0.048  -1.362  -0.205  1.00  0.00
ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00

Double-Quotes Around Arguments

For the same reason that we put the loop variable inside double-quotes, in case the filename happens to contain any spaces, we surround $1 with double-quotes.

Currently, we need to edit middle.sh each time we want to adjust the range of lines that is returned. Let’s fix that by configuring our script to instead use three command-line arguments. After the first command-line argument ($1), each additional argument that we provide will be accessible via the special variables $1, $2, $3, which refer to the first, second, third command-line arguments, respectively.

Knowing this, we can use additional arguments to define the range of lines to be passed to head and tail respectively:

$ nano middle.sh

head -n "$2" "$1" | tail -n "$3"

We can now run:

$ bash middle.sh pentane.pdb 15 5

ATOM      9  H           1       1.324   0.350  -1.332  1.00  0.00
ATOM     10  H           1       1.271   1.378   0.122  1.00  0.00
ATOM     11  H           1      -0.074  -0.384   1.288  1.00  0.00
ATOM     12  H           1      -0.048  -1.362  -0.205  1.00  0.00
ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00

By changing the arguments to our command we can change our script’s behaviour:

$ bash middle.sh pentane.pdb 20 5

ATOM     14  H           1      -1.259   1.420   0.112  1.00  0.00
ATOM     15  H           1      -2.608  -0.407   1.130  1.00  0.00
ATOM     16  H           1      -2.540  -1.303  -0.404  1.00  0.00
ATOM     17  H           1      -3.393   0.254  -0.321  1.00  0.00
TER      18              1

This works, but it may take the next person who reads middle.sh a moment to figure out what it does. We can improve our script by adding some comments at the top:

$ nano middle.sh

# Select lines from the middle of a file.
# Usage: bash middle.sh filename end_line num_lines
head -n "$2" "$1" | tail -n "$3"

A comment starts with a # character and runs to the end of the line. The computer ignores comments, but they’re invaluable for helping people (including your future self) understand and use scripts. The only caveat is that each time you modify the script, you should check that the comment is still accurate: an explanation that sends the reader in the wrong direction is worse than none at all.

What if we want to process many files in a single pipeline? For example, if we want to sort our .pdb files by length, we would type:

$ wc -l *.pdb | sort -n

because wc -l lists the number of lines in the files (recall that wc stands for ‘word count’, adding the -l option means ‘count lines’ instead) and sort -n sorts things numerically. We could put this in a file, but then it would only ever sort a list of .pdb files in the current directory. If we want to be able to get a sorted list of other kinds of files, we need a way to get all those names into the script. We can’t use $1, $2, and so on because we don’t know how many files there are. Instead, we use the special variable $@, which means, ‘All of the command-line arguments to the shell script’. We also should put $@ inside double-quotes to handle the case of arguments containing spaces ("$@" is special syntax and is equivalent to "$1" "$2" …).

Here’s an example:

$ nano sorted.sh

# Sort files by their length.
# Usage: bash sorted.sh one_or_more_filenames
wc -l "$@" | sort -n

$ bash sorted.sh *.pdb ../creatures/*.dat

methane.pdb
ethane.pdb
propane.pdb
cubane.pdb
pentane.pdb
octane.pdb
../creatures/basilisk.dat
../creatures/minotaur.dat
../creatures/unicorn.dat
total

List Unique Species

Leah has several hundred data files, each of which is formatted like this:
2013-11-05,deer,5
2013-11-05,rabbit,22
2013-11-05,raccoon,7
2013-11-06,rabbit,19
2013-11-06,deer,2
2013-11-06,fox,1
2013-11-07,rabbit,18
2013-11-07,bear,1
An example of this type of file is given in shell-lesson-data/exercise-data/animal-counts/animals.csv.

We can use the command cut -d , -f 2 animals.txt | sort | uniq to produce the unique species in animals.txt. In order to avoid having to type out this series of commands every time, a scientist may choose to write a shell script instead.

Write a shell script called species.sh that takes any number of filenames as command-line arguments, and uses a variation of the above command to print a list of the unique species appearing in each of those files separately.
Solution
# Script to find unique species in csv files where species is the second data field
# This script accepts any number of file names as command line arguments

# Loop over all files
for file in "$@"
do
    echo "Unique species in $file:"
    # Extract species names
    cut -d , -f 2 "$file" | sort | uniq
done

Suppose we have just run a series of commands that did something useful — for example, that created a graph we’d like to use in a paper. We’d like to be able to re-create the graph later if we need to, so we want to save the commands in a file. Instead of typing them in again (and potentially getting them wrong) we can do this:

$ history | tail -n 5 > redo-figure-3.sh

The file redo-figure-3.sh now contains:

bash goostats.sh NENE01729B.txt stats-NENE01729B.txt
bash goodiff.sh stats-NENE01729B.txt /data/validated/01729.txt > 01729-differences.txt
cut -d ',' -f 2-3 01729-differences.txt > 01729-time-series.txt
ygraph --format scatter --color bw --borders none 01729-time-series.txt figure-3.png
history | tail -n 5 > redo-figure-3.sh

After a moment’s work in an editor to remove the serial numbers on the commands, and to remove the final line where we called the history command, we have a completely accurate record of how we created that figure.

Why Record Commands in the History Before Running Them?

If you run the command:
$ history | tail -n 5 > recent.sh
the last command in the file is the history command itself, i.e., the shell has added history to the command log before actually running it. In fact, the shell always adds commands to the log before running them. Why do you think it does this?

Solution

If a command causes something to crash or hang, it might be useful to know what that command was, in order to investigate the problem. Were the command only be recorded after running it, we would not have a record of the last command run in the event of a crash.

In practice, most people develop shell scripts by running commands at the shell prompt a few times to make sure they’re doing the right thing, then saving them in a file for re-use. This style of work allows people to recycle what they discover about their data and their workflow with one call to history and a bit of editing to clean up the output and save it as a shell script.

Nelle’s Pipeline: Creating a Script

Nelle’s supervisor insisted that all her analytics must be reproducible. The easiest way to capture all the steps is in a script.

First we return to Nelle’s project directory:

$ cd ../../north-pacific-gyre/

She creates a file using nano …

$ nano do-stats.sh

…which contains the following:

# Calculate stats for data files.
for datafile in "$@"
do
    echo $datafile
    bash goostats.sh $datafile stats-$datafile
done

She saves this in a file called do-stats.sh so that she can now re-do the first stage of her analysis by typing:

$ bash do-stats.sh NENE*A.txt NENE*B.txt

She can also do this:

$ bash do-stats.sh NENE*A.txt NENE*B.txt | wc -l

so that the output is just the number of files processed rather than the names of the files that were processed.

One thing to note about Nelle’s script is that it lets the person running it decide what files to process. She could have written it as:

# Calculate stats for Site A and Site B data files.
for datafile in NENE*A.txt NENE*B.txt
do
    echo $datafile
    bash goostats.sh $datafile stats-$datafile
done

The advantage is that this always selects the right files: she doesn’t have to remember to exclude the ‘Z’ files. The disadvantage is that it always selects just those files — she can’t run it on all files (including the ‘Z’ files), or on the ‘G’ or ‘H’ files her colleagues in Antarctica are producing, without editing the script. If she wanted to be more adventurous, she could modify her script to check for command-line arguments, and use NENE*A.txt NENE*B.txt if none were provided. Of course, this introduces another tradeoff between flexibility and complexity.

Variables in Shell Scripts

In the proteins directory, imagine you have a shell script called script.sh containing the following commands:
head -n $2 $1
tail -n $3 $1
While you are in the proteins directory, you type the following command:
$ bash script.sh '*.pdb' 1 1
Which of the following outputs would you expect to see?

All of the lines between the first and the last lines of each file ending in .pdb in the proteins directory

The first and the last line of each file ending in .pdb in the proteins directory

The first and the last line of each file in the proteins directory

An error because of the quotes around *.pdb
Solution

The correct answer is 2.

The special variables $1, $2 and $3 represent the command line arguments given to the script, such that the commands run are:
$ head -n 1 cubane.pdb ethane.pdb octane.pdb pentane.pdb propane.pdb
$ tail -n 1 cubane.pdb ethane.pdb octane.pdb pentane.pdb propane.pdb
The shell does not expand '*.pdb' because it is enclosed by quote marks. As such, the first argument to the script is '*.pdb' which gets expanded within the script by head and tail.

Find the Longest File With a Given Extension

Write a shell script called longest.sh that takes the name of a directory and a filename extension as its arguments, and prints out the name of the file with the most lines in that directory with that extension. For example:
$ bash longest.sh shell-lesson-data/exercise-data/proteins pdb
would print the name of the .pdb file in shell-lesson-data/exercise-data/proteins that has the most lines.

Feel free to test your script on another directory e.g.
$ bash longest.sh shell-lesson-data/exercise-data/writing txt
Solution
# Shell script which takes two arguments:
#    1. a directory name
#    2. a file extension
# and prints the name of the file in that directory
# with the most lines which matches the file extension.

wc -l $1/*.$2 | sort -n | tail -n 2 | head -n 1
The first part of the pipeline, wc -l $1/*.$2 | sort -n, counts the lines in each file and sorts them numerically (largest last). When there’s more than one file, wc also outputs a final summary line, giving the total number of lines across all files. We use tail -n 2 | head -n 1 to throw away this last line.

With wc -l $1/*.$2 | sort -n | tail -n 1 we’ll see the final summary line: we can build our pipeline up in pieces to be sure we understand the output.

Script Reading Comprehension

For this question, consider the shell-lesson-data/exercise-data/proteins directory once again. This contains a number of .pdb files in addition to any other files you may have created. Explain what each of the following three scripts would do when run as bash script1.sh *.pdb, bash script2.sh *.pdb, and bash script3.sh *.pdb respectively.
# Script 1
echo *.*
# Script 2
for filename in $1 $2 $3
do
    cat $filename
done
# Script 3
echo $@.pdb
Solutions

In each case, the shell expands the wildcard in *.pdb before passing the resulting list of file names as arguments to the script.

Script 1 would print out a list of all files containing a dot in their name. The arguments passed to the script are not actually used anywhere in the script.

Script 2 would print the contents of the first 3 files with a .pdb file extension. $1, $2, and $3 refer to the first, second, and third argument respectively.

Script 3 would print all the arguments to the script (i.e. all the .pdb files), followed by .pdb. $@ refers to all the arguments given to a shell script.
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb.pdb

Debugging Scripts

Suppose you have saved the following script in a file called do-errors.sh in Nelle’s north-pacific-gyre directory:
# Calculate stats for data files.
for datafile in "$@"
do
    echo $datfile
    bash goostats.sh $datafile stats-$datafile
done
When you run it from the north-pacific-gyre directory:
$ bash do-errors.sh NENE*A.txt NENE*B.txt
the output is blank. To figure out why, re-run the script using the -x option:
$ bash -x do-errors.sh NENE*A.txt NENE*B.txt
What is the output showing you? Which line is responsible for the error?

Solution

The -x option causes bash to run in debug mode. This prints out each command as it is run, which will help you to locate errors. In this example, we can see that echo isn’t printing anything. We have made a typo in the loop variable name, and the variable datfile doesn’t exist, hence returning an empty string.

Key Points

Save commands in files (usually called shell scripts) for re-use.

bash [filename] runs the commands saved in a file.

$@ refers to all of a shell script’s command-line arguments.

$1, $2, etc., refer to the first command-line argument, the second command-line argument, etc.

Place variables in quotes if the values might have spaces in them.

Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.

Shell Variables

Overview

Teaching: 10 min
Exercises: 0 min

Questions

How are variables set and accessed in the Unix shell?

Objectives

Understand how variables are implemented in the shell

Explain how the shell uses the PATH variable to search for executables

Read the value of an existing variable

Create new variables and change their values

Understand child process and the export of variables

The shell is just a program, and like other programs, it has variables. Those variables control its execution, so by changing their values you can change how the shell and other programs behave.

Let’s start by running the command set and looking at some of the variables in a typical shell session:

$ set

COMPUTERNAME=TURING
HOME=/home/vlad
HOMEDRIVE=C:
HOSTNAME=TURING
HOSTTYPE=i686
NUMBER_OF_PROCESSORS=4
OS=Windows_NT
PATH=/Users/vlad/bin:/usr/local/git/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
PWD=/home/vlad
UID=1000
USERNAME=vlad
...

As you can see, there are quite a few—in fact, four or five times more than what’s shown here. And yes, using set to show things might seem a little strange, even for Unix, but if you don’t give it any arguments, it might as well show you things you could set.

Every variable has a name. By convention, variables that are always present are given upper-case names. All shell variables’ values are strings, even those (like UID) that look like numbers. It’s up to programs to convert these strings to other types when necessary. For example, if a program wanted to find out how many processors the computer had, it would convert the value of the NUMBER_OF_PROCESSORS variable from a string to an integer.

Similarly, some variables (like PATH) store lists of values. In this case, the convention is to use a colon ‘:’ as a separator. If a program wants the individual elements of such a list, it’s the program’s responsibility to split the variable’s string value into pieces.

The `PATH` Variable

Let’s have a closer look at that PATH variable. Its value defines the shell’s search path, i.e., the list of directories that the shell looks in for runnable programs when you type in a program name without specifying what directory it is in.

For example, when we type a command like analyze, the shell needs to decide whether to run ./analyze or /bin/analyze. The rule it uses is simple: the shell checks each directory in the PATH variable in turn, looking for a program with the requested name in that directory. As soon as it finds a match, it stops searching and runs the program.

To show how this works, here are the components of PATH listed one per line:

/Users/vlad/bin
/usr/local/git/bin
/usr/bin
/bin
/usr/sbin
/sbin
/usr/local/bin

On our computer, there are actually three programs called analyze in three different directories: /bin/analyze, /usr/local/bin/analyze, and /users/vlad/analyze. Since the shell searches the directories in the order they’re listed in PATH, it finds /bin/analyze first and runs that. Notice that it will never find the program /users/vlad/analyze unless we type in the full path to the program, since the directory /users/vlad isn’t in PATH.

Showing the Value of a Variable

Let’s show the value of the variable HOME:

$ echo HOME

HOME

That just prints “HOME”, which isn’t what we wanted (though it is what we actually asked for). Let’s try this instead:

$ echo $HOME

/home/vlad

The dollar sign tells the shell that we want the value of the variable rather than its name. This works just like wildcards: the shell does the replacement before running the program we’ve asked for. Thanks to this expansion, what we actually run is echo /home/vlad, which displays the right thing.

Creating and Changing Variables

Creating a variable is easy—we just assign a value to a name using “=”:

$ SECRET_IDENTITY=Dracula
$ echo $SECRET_IDENTITY

Dracula

To change the value, just assign a new one:

$ SECRET_IDENTITY=Camilla
$ echo $SECRET_IDENTITY

Camilla

If we want to set some variables automatically every time we run a shell, we can put commands to do this in a file called .bashrc in our home directory. (The ‘.’ character at the front prevents ls from listing this file unless we specifically ask it to using -a: we normally don’t want to worry about it. The “rc” at the end is an abbreviation for “run control”, which meant something really important decades ago, and is now just a convention everyone follows without understanding why.)

For example, here are two lines in /home/vlad/.bashrc:

export SECRET_IDENTITY=Dracula
export TEMP_DIR=/tmp
export BACKUP_DIR=$TEMP_DIR/backup

These three lines create the variables SECRET_IDENTITY, TEMP_DIR, and BACKUP_DIR, and export them so that any programs the shell runs can see them as well. Notice that BACKUP_DIR’s definition relies on the value of TEMP_DIR, so that if we change where we put temporary files, our backups will be relocated automatically.

While we’re here, it’s also common to use the alias command to create shortcuts for things we frequently type. For example, we can define the alias backup to run /bin/zback with a specific set of arguments:

alias backup='/bin/zback -v --nostir -R 20000 $HOME $BACKUP_DIR'

As you can see, aliases can save us a lot of typing, and hence a lot of typing mistakes. You can find interesting suggestions for other aliases and other bash tricks by searching for “sample bashrc” in your favorite search engine.

Child Processes and `export`

A running command is called a process. All processes are created by other processes. Most of the time you are using your running bash process to launch processes by typing commands. Each of these processs can be called a child process of your bash shell pprocess. A child process is started with all the variables marked for export in the parent process. Remember our pipe and filter example, let’s put the bash process in the picture too.

Child process

You can see the effect of using export by starting a child bash process. First let’s set two variables, one exported and the other not.

Export control

$ export X="Hello, anyone there?"
$ Y="I'm over here."
$ echo $X $Y

Hello, anyone there? I'm over here.

Start a bash child process and echo the same variables.

$ bash
$ echo $X $Y

Hello, anyone there?

The Y variable was not exported to the child bash process so does not show up.

Key Points

Shell variables are by default treated as strings

The PATH variable defines the shell’s search path

Variables are assigned using “=” and recalled using the variable’s name prefixed by “$”

Only exported variables make it into the environment of child processes

BREAK

Overview

Teaching: 15 min
Exercises: 0 min

Questions

🥤 Coffee or 🫖 Tea?

Objectives

Make sure we are not too overloaded

Key Points

Finding Things

Overview

Teaching: 25 min
Exercises: 20 min

Questions

How can I find files?

How can I find things in files?

Objectives

Use grep to select lines from text files that match simple patterns.

Use find to find files and directories whose names match simple patterns.

Use the output of one command as the command-line argument(s) to another command.

Explain what is meant by ‘text’ and ‘binary’ files, and why many common tools don’t handle the latter well.

In the same way that many of us now use ‘Google’ as a verb meaning ‘to find’, Unix programmers often use the word ‘grep’. ‘grep’ is a contraction of ‘global/regular expression/print’, a common sequence of operations in early Unix text editors. It is also the name of a very useful command-line program.

grep finds and prints lines in files that match a pattern. For our examples, we will use a file that contains three haiku taken from a 1998 competition in Salon magazine. For this set of examples, we’re going to be working in the writing subdirectory:

$ cd
$ cd Desktop/shell-lesson-data/exercise-data/writing
$ cat haiku.txt

The Tao that is seen
Is not the true Tao, until
You bring fresh toner.

With searching comes loss
and the presence of absence:
"My Thesis" not found.

Yesterday it worked
Today it is not working
Software is like that.

Forever, or Five Years

We haven’t linked to the original haiku because they don’t appear to be on Salon’s site any longer. As Jeff Rothenberg said, ‘Digital information lasts forever — or five years, whichever comes first.’ Luckily, popular content often has backups.

Let’s find lines that contain the word ‘not’:

$ grep not haiku.txt

Is not the true Tao, until
"My Thesis" not found
Today it is not working

Here, not is the pattern we’re searching for. The grep command searches through the file, looking for matches to the pattern specified. To use it type grep, then the pattern we’re searching for and finally the name of the file (or files) we’re searching in.

The output is the three lines in the file that contain the letters ‘not’.

By default, grep searches for a pattern in a case-sensitive way. In addition, the search pattern we have selected does not have to form a complete word, as we will see in the next example.

Let’s search for the pattern: ‘The’.

$ grep The haiku.txt

The Tao that is seen
"My Thesis" not found.

This time, two lines that include the letters ‘The’ are outputted, one of which contained our search pattern within a larger word, ‘Thesis’.

To restrict matches to lines containing the word ‘The’ on its own, we can give grep with the -w option. This will limit matches to word boundaries.

Later in this lesson, we will also see how we can change the search behavior of grep with respect to its case sensitivity.

$ grep -w The haiku.txt

The Tao that is seen

Note that a ‘word boundary’ includes the start and end of a line, so not just letters surrounded by spaces. Sometimes we don’t want to search for a single word, but a phrase. This is also easy to do with grep by putting the phrase in quotes.

$ grep -w "is not" haiku.txt

Today it is not working

We’ve now seen that you don’t have to have quotes around single words, but it is useful to use quotes when searching for multiple words. It also helps to make it easier to distinguish between the search term or phrase and the file being searched. We will use quotes in the remaining examples.

Another useful option is -n, which numbers the lines that match:

$ grep -n "it" haiku.txt

With searching comes loss
Yesterday it worked
Today it is not working

Here, we can see that lines 5, 9, and 10 contain the letters ‘it’.

We can combine options (i.e. flags) as we do with other Unix commands. For example, let’s find the lines that contain the word ‘the’. We can combine the option -w to find the lines that contain the word ‘the’ and -n to number the lines that match:

$ grep -n -w "the" haiku.txt

2:Is not the true Tao, until
6:and the presence of absence:

Now we want to use the option -i to make our search case-insensitive:

$ grep -n -w -i "the" haiku.txt

The Tao that is seen
Is not the true Tao, until
and the presence of absence:

Now, we want to use the option -v to invert our search, i.e., we want to output the lines that do not contain the word ‘the’.

$ grep -n -w -v "the" haiku.txt

The Tao that is seen
You bring fresh toner.

With searching comes loss
"My Thesis" not found.

Yesterday it worked
Today it is not working
Software is like that.

If we use the -r (recursive) option, grep can search for a pattern recursively through a set of files in subdirectories.

Let’s search recursively for Yesterday in the shell-lesson-data/exercise-data/writing directory. (Recall that . means the current directory.)

$ grep -r Yesterday .

./LittleWomen.txt:"Yesterday, when Aunt was asleep and I was trying to be as still as a
./LittleWomen.txt:Yesterday at dinner, when an Austrian officer stared at us and then
./LittleWomen.txt:Yesterday was a quiet day spent in teaching, sewing, and writing in my
./haiku.txt:Yesterday it worked

grep has lots of other options. To find out what they are, we can type:

$ grep --help

Usage: grep [OPTION]... PATTERN [FILE]...
Search for PATTERN in each FILE or standard input.
PATTERN is, by default, a basic regular expression (BRE).
Example: grep -i 'hello world' menu.h main.c

Regexp selection and interpretation:
  -E, --extended-regexp     PATTERN is an extended regular expression (ERE)
  -F, --fixed-strings       PATTERN is a set of newline-separated fixed strings
  -G, --basic-regexp        PATTERN is a basic regular expression (BRE)
  -P, --perl-regexp         PATTERN is a Perl regular expression
  -e, --regexp=PATTERN      use PATTERN for matching
  -f, --file=FILE           obtain PATTERN from FILE
  -i, --ignore-case         ignore case distinctions
  -w, --word-regexp         force PATTERN to match only whole words
  -x, --line-regexp         force PATTERN to match only whole lines
  -z, --null-data           a data line ends in 0 byte, not newline

Miscellaneous:
...        ...        ...

Using grep

Which command would result in the following output:
and the presence of absence:
grep "of" haiku.txt

grep -E "of" haiku.txt

grep -w "of" haiku.txt

grep -i "of" haiku.txt

Solution

The correct answer is 3, because the -w option looks only for whole-word matches. The other options will also match ‘of’ when part of another word.

Wildcards

grep’s real power doesn’t come from its options, though; it comes from the fact that patterns can include wildcards. (The technical name for these is regular expressions, which is what the ‘re’ in ‘grep’ stands for.) Regular expressions are both complex and powerful; if you want to do complex searches, please look at the lesson on the Software Carpentry website. As a taster, we can find lines that have an ‘o’ in the second position like this:
$ grep -E "^.o" haiku.txt
You bring fresh toner.
Today it is not working
Software is like that.
We use the -E option and put the pattern in quotes to prevent the shell from trying to interpret it. (If the pattern contained a *, for example, the shell would try to expand it before running grep.) The ^ in the pattern anchors the match to the start of the line. The . matches a single character (just like ? in the shell), while the o matches an actual ‘o’.

Tracking a Species

Leah has several hundred data files saved in one directory, each of which is formatted like this:
2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-06,fox,4
2012-11-07,rabbit,16
2012-11-07,bear,1
She wants to write a shell script that takes a species (for example rabbit) as the first command-line argument and a directory (for example .) as the second argument. The script should return one file called <species>.txt containing a list of dates and the number of that species seen on each date. For example using the data shown above, rabbit.txt would contain:
2012-11-05,22
2012-11-06,19
2012-11-07,16
Below, each line contains an individual command, or pipe. Arrange their sequence in one command in order to achieve Leah’s goal:
cut -d : -f 2
>
|
grep -w $1 -r $2
|
$1.txt
cut -d , -f 1,3
Hint: use man grep to look for how to grep text recursively in a directory and man cut to select more than one field in a line.

An example of such a file is provided in shell-lesson-data/exercise-data/animal-counts/animals.csv
Solution
grep -w $1 -r $2 | cut -d : -f 2 | cut -d , -f 1,3 > $1.txt
Actually, you can swap the order of the two cut commands and it still works. At the command line, try changing the order of the cut commands, and have a look at the output from each step to see why this is the case.

You would call the script above like this:
$ bash count-species.sh bear .

Little Women

You and your friend, having just finished reading Little Women by Louisa May Alcott, are in an argument. Of the four sisters in the book, Jo, Meg, Beth, and Amy, your friend thinks that Jo was the most mentioned. You, however, are certain it was Amy. Luckily, you have a file LittleWomen.txt containing the full text of the novel (shell-lesson-data/exercise-data/writing/LittleWomen.txt). Using a for loop, how would you tabulate the number of times each of the four sisters is mentioned?

Hint: one solution might employ the commands grep and wc and a |, while another might utilize grep options. There is often more than one way to solve a programming task, so a particular solution is usually chosen based on a combination of yielding the correct result, elegance, readability, and speed.
Solutions
for sis in Jo Meg Beth Amy
do
    echo $sis:
    grep -ow $sis LittleWomen.txt | wc -l
done
Alternative, slightly inferior solution:
for sis in Jo Meg Beth Amy
do
    echo $sis:
    grep -ocw $sis LittleWomen.txt
done
This solution is inferior because grep -c only reports the number of lines matched. The total number of matches reported by this method will be lower if there is more than one match per line.

Perceptive observers may have noticed that character names sometimes appear in all-uppercase in chapter titles (e.g. ‘MEG GOES TO VANITY FAIR’). If you wanted to count these as well, you could add the -i option for case-insensitivity (though in this case, it doesn’t affect the answer to which sister is mentioned most frequently).

While grep finds lines in files, the find command finds files themselves. Again, it has a lot of options; to show how the simplest ones work, we’ll use the shell-lesson-data/exercise-data directory tree shown below.

.
├── animal-counts/
│   └── animals.csv
├── creatures/
│   ├── basilisk.dat
│   ├── minotaur.dat
│   └── unicorn.dat
├── numbers.txt
├── proteins/
│   ├── cubane.pdb
│   ├── ethane.pdb
│   ├── methane.pdb
│   ├── octane.pdb
│   ├── pentane.pdb
│   └── propane.pdb
└── writing/
    ├── haiku.txt
    └── LittleWomen.txt

The exercise-data directory contains one file, numbers.txt and four directories: animal-counts, creatures, proteins and writing containing various files.

For our first command, let’s run find . (remember to run this command from the shell-lesson-data/exercise-data folder).

$ find .

.
./writing
./writing/LittleWomen.txt
./writing/haiku.txt
./creatures
./creatures/basilisk.dat
./creatures/unicorn.dat
./creatures/minotaur.dat
./animal-counts
./animal-counts/animals.csv
./numbers.txt
./proteins
./proteins/ethane.pdb
./proteins/propane.pdb
./proteins/octane.pdb
./proteins/pentane.pdb
./proteins/methane.pdb
./proteins/cubane.pdb

(You should see something similar, but not necessarily in the same order.)

As always, the . on its own means the current working directory, which is where we want our search to start. find’s output is the names of every file and directory under the current working directory. This can seem useless at first but find has many options to filter the output and in this lesson we will discover some of them.

The first option in our list is -type d that means ‘things that are directories’. Sure enough, find’s output is the names of the five directories (including .):

$ find . -type d

.
./writing
./creatures
./animal-counts
./proteins

Notice that the objects find finds are not listed in any particular order. If we change -type d to -type f, we get a listing of all the files instead:

$ find . -type f

./writing/LittleWomen.txt
./writing/haiku.txt
./creatures/basilisk.dat
./creatures/unicorn.dat
./creatures/minotaur.dat
./animal-counts/animals.csv
./numbers.txt
./proteins/ethane.pdb
./proteins/propane.pdb
./proteins/octane.pdb
./proteins/pentane.pdb
./proteins/methane.pdb
./proteins/cubane.pdb

Now let’s try matching by name:

$ find . -name *.txt

./numbers.txt

We expected it to find all the text files, but it only prints out ./numbers.txt. The problem is that the shell expands wildcard characters like * before commands run. Since *.txt in the current directory expands to ./numbers.txt, the command we actually ran was:

$ find . -name numbers.txt

find did what we asked; we just asked for the wrong thing.

To get what we want, let’s do what we did with grep: put *.txt in quotes to prevent the shell from expanding the * wildcard. This way, find actually gets the pattern *.txt, not the expanded filename numbers.txt:

$ find . -name "*.txt"

./writing/LittleWomen.txt
./writing/haiku.txt
./numbers.txt

Listing vs. Finding

ls and find can be made to do similar things given the right options, but under normal circumstances, ls lists everything it can, while find searches for things with certain properties and shows them.

As we said earlier, the command line’s power lies in combining tools. We’ve seen how to do that with pipes; let’s look at another technique. As we just saw, find . -name "*.txt" gives us a list of all text files in or below the current directory. How can we combine that with wc -l to count the lines in all those files?

The simplest way is to put the find command inside $():

$ wc -l $(find . -name "*.txt")

./writing/LittleWomen.txt
./writing/haiku.txt
./numbers.txt
total

When the shell executes this command, the first thing it does is run whatever is inside the $(). It then replaces the $() expression with that command’s output. Since the output of find is the three filenames ./writing/LittleWomen.txt, ./writing/haiku.txt, and ./numbers.txt, the shell constructs the command:

$ wc -l ./writing/LittleWomen.txt ./writing/haiku.txt ./numbers.txt

which is what we wanted. This expansion is exactly what the shell does when it expands wildcards like * and ?, but lets us use any command we want as our own ‘wildcard’.

It’s very common to use find and grep together. The first finds files that match a pattern; the second looks for lines inside those files that match another pattern. Here, for example, we can find txt files that contain the word “searching” by looking for the string ‘searching’ in all the .txt files in the current directory:

$ grep "searching" $(find . -name "*.txt")

./writing/LittleWomen.txt:sitting on the top step, affected to be searching for her book, but was
./writing/haiku.txt:With searching comes loss

Matching and Subtracting

The -v option to grep inverts pattern matching, so that only lines which do not match the pattern are printed. Given that, which of the following commands will find all .dat files in creatures except unicorn.dat? Once you have thought about your answer, you can test the commands in the shell-lesson-data/exercise-data directory.

find creatures -name "*.dat" | grep -v unicorn

find creatures -name *.dat | grep -v unicorn

grep -v "unicorn" $(find creatures -name "*.dat")

None of the above.

Solution

Option 1 is correct. Putting the match expression in quotes prevents the shell expanding it, so it gets passed to the find command.

Option 2 is also works in this instance because the shell tries to expand *.dat but there are no *.dat files in the current directory, so the wildcard expression gets passed to find. We first encountered this in episode 3.

Option 3 is incorrect because it searches the contents of the files for lines which do not match ‘unicorn’, rather than searching the file names.

Binary Files

We have focused exclusively on finding patterns in text files. What if your data is stored as images, in databases, or in some other format?

A handful of tools extend grep to handle a few non text formats. But a more generalizable approach is to convert the data to text, or extract the text-like elements from the data. On the one hand, it makes simple things easy to do. On the other hand, complex things are usually impossible. For example, it’s easy enough to write a program that will extract X and Y dimensions from image files for grep to play with, but how would you write something to find values in a spreadsheet whose cells contained formulas?

A last option is to recognize that the shell and text processing have their limits, and to use another programming language when appropriate. When the time comes to do this, don’t be too hard on the shell: many modern programming languages have borrowed a lot of ideas from it, and imitation is also the sincerest form of praise.

The Unix shell is older than most of the people who use it. It has survived so long because it is one of the most productive programming environments ever created — maybe even the most productive. Its syntax may be cryptic, but people who have mastered it can experiment with different commands interactively, then use what they have learned to automate their work. Graphical user interfaces may be easier to use at first, but once learned, the productivity in the shell is unbeatable. And as Alfred North Whitehead wrote in 1911, ‘Civilization advances by extending the number of important operations which we can perform without thinking about them.’

find Pipeline Reading Comprehension

Write a short explanatory comment for the following shell script:
wc -l $(find . -name "*.dat") | sort -n
Solution

Find all files with a .dat extension recursively from the current directory

Count the number of lines each of these files contains

Sort the output from step 2 numerically

Key Points

find finds files with specific properties that match patterns.

grep selects lines in files that match patterns.

--help is an option supported by many bash commands, and programs that can be run from within Bash, to display more information on how to use these commands or programs.

man [command] displays the manual page for a given command.

$([command]) inserts a command’s output in place.

Working Remotely

Overview

Teaching: 10 min
Exercises: 0 min

Questions

How do I use ‘ssh’ and ‘scp’ ?

Objectives

Learn what SSH is

Learn what an SSH key is

Generate your own SSH key pair

Learn how to use your SSH key

Learn how to work remotely using ssh and scp

Add your SSH key to an remote server

Let’s take a closer look at what happens when we use the shell on a desktop or laptop computer. The first step is to log in so that the operating system knows who we are and what we’re allowed to do. We do this by typing our username and password; the operating system checks those values against its records, and if they match, runs a shell for us.

As we type commands, the 1’s and 0’s that represent the characters we’re typing are sent from the keyboard to the shell. The shell displays those characters on the screen to represent what we type, and then, if what we typed was a command, the shell executes it and displays its output (if any).

What if we want to run some commands on another machine, such as the server in the basement that manages our database of experimental results? To do this, we have to first log in to that machine. We call this a remote login.

In order for us to be able to login, the remote computer must be running a remote login server and we will run a client program that can talk to that server. The client program passes our login credentials to the remote login server and, if we are allowed to login, that server then runs a shell for us on the remote computer.

Once our local client is connected to the remote server, everything we type into the client is passed on, by the server, to the shell running on the remote computer. That remote shell runs those commands on our behalf, just as a local shell would, then sends back output, via the server, to our client, for our computer to display.

SSH History

Back in the day, when everyone trusted each other and knew every chip in their computer by its first name, people didn’t encrypt anything except the most sensitive information when sending it over a network and the two programs used for running a shell (usually back then, the Bourne Shell, sh) on, or copying files to, a remote machine were named rsh and rcp, respectively. Think (r)emote sh and cp

However, anyone could watch the unencrypted network traffic, which meant that villains could steal usernames and passwords, and use them for all manner of nefarious purposes.

The SSH protocol was invented to prevent this (or at least slow it down). It uses several sophisticated, and heavily tested, encryption protocols to ensure that outsiders can’t see what’s in the messages going back and forth between different computers.

The remote login server which accepts connections from client programs is known as the SSH daemon, or sshd.

The client program we use to login remotely is the secure shell, or ssh, think (s)ecure sh.

The ssh login client has a companion program called scp, think (s)ecure cp, which allows us to copy files to or from a remote computer using the same kind of encrypted connection.

A remote login using `ssh`

To make a remote login, we issue the command ssh username@computer which tries to make a connection to the SSH daemon running on the remote computer we have specified.

After we log in, we can use the remote shell to use the remote computer’s files and directories.

Typing exit or Control-D terminates the remote shell, and the local client program, and returns us to our previous shell.

In the example below, the remote machine’s command prompt is moon> instead of just $. To make it clearer which machine is doing what, we’ll indent the commands sent to the remote machine and their output.

$ pwd

/users/vlad

$ ssh vlad@moon.euphoric.edu
Password: ********

    moon> hostname

    moon

    moon> pwd

    /home/vlad

    moon> ls -F

    bin/     cheese.txt   dark_side/   rocks.cfg

    moon> exit

$ pwd

/users/vlad

Copying files to, and from a remote machine using `scp`

To copy a file, we specify the source and destination paths, either of which may include computer names. If we leave out a computer name, scp assumes we mean the machine we’re running on. For example, this command copies our latest results to the backup server in the basement, printing out its progress as it does so:

$ scp results.dat vlad@backupserver:backups/results-2011-11-11.dat
Password: ********

results.dat              100%  9  1.0 MB/s 00:00

Note the colon :, seperating the hostname of the server and the pathname of the file we are copying to. It is this character that informs scp that the source or target of the copy is on the remote machine and the reason it is needed can be explained as follows:

In the same way that the default directory into which we are placed when running a shell on a remote machine is our home directory on that machine, the default target, for a remote copy, is also the home directory.

This means that

$ scp results.dat vlad@backupserver:

would copy results.dat into our home directory on backupserver, however, if we did not have the colon to inform scp of the remote machine, we would still have a valid commmad

$ scp results.dat vlad@backupserver

but now we have merely created a file called vlad@backupserver on our local machine, as we would have done with cp.

$ cp results.dat vlad@backupserver

Copying a whole directory betwen remote machines uses the same syntax as the cp command: we just use the -r option to signal that we want copying to be recursive. For example, this command copies all of our results from the backup server to our laptop:

$ scp -r vlad@backupserver:backups ./backups
Password: ********

results-2011-09-18.dat              100%  7  1.0 MB/s 00:00
results-2011-10-04.dat              100%  9  1.0 MB/s 00:00
results-2011-10-28.dat              100%  8  1.0 MB/s 00:00
results-2011-11-11.dat              100%  9  1.0 MB/s 00:00

rsync

rsync copies files over the network (or locally) much like scp. It is however more intelligent in its approach. Where destination files already exist, it copies only what is required to update any differences. You can use it to push / pull files over ssh.

To pull data from a remote host, use:
$ rsync user@host:remote_path local_path 
and to push data to a remote host, use:
$ rsync local_path user@host:remote_path
As with scp it requires no special configuration (though remember to set up ssh keys) and has a very similar syntax, e.g. remote path is relative to home directory unless starts with /

Useful flags for rsync:

-r (recursive) – go down the directory tree copying stuff.

-c (checksum) – when deciding what files to send, look not only at size and timestamp but if necessary also file contents

--delete – remove files from destination not present at source end. (Test with -n first!)

-v (verbose) – list files that are transferred (or deleted)

-n (dry run) – go through the motions but do not actually transfer (or delete) files. Useful with -v.

-a (archive) – copy recursively and try to copy permissions, ownership, etc.

Running commands on a remote machine using `ssh`

Here’s one more thing the ssh client program can do for us. Suppose we want to check whether we have already created the file backups/results-2011-11-12.dat on the backup server. Instead of logging in and then typing ls, we could do this:

$ ssh vlad@backupserver "ls results*"
Password: ********

results-2011-09-18.dat  results-2011-10-28.dat
results-2011-10-04.dat  results-2011-11-11.dat

Here, ssh takes the argument after our remote username and passes them to the shell on the remote computer. (We have to put quotes around it to make it look like a single argument.) Since those arguments are a legal command, the remote shell runs ls results for us and sends the output back to our local shell for display.

SSH Keys

Typing our password over and over again is annoying, especially if the commands we want to run remotely are in a loop. To remove the need to do this, we can create an SSH key to tell the remote machine that it should always trust us.

SSH keys come in pairs, a public key that gets shared with services like GitHub, and a private key that is stored only on your computer. If the keys match, you’re granted access.

The cryptography behind SSH keys ensures that no one can reverse engineer your private key from the public one.

The first step in using SSH authorization is to generate your own key pair.

You might already have an SSH key pair on your machine. You can check to see if one exists by moving to your .ssh directory and listing the contents.

$ cd ~/.ssh
$ ls

If you see id_rsa.pub, you already have a key pair and don’t need to create a new one.

If you don’t see id_rsa.pub, use the following command to generate a new key pair. Make sure to replace your@email.com with your own email address.

$ ssh-keygen -t rsa -C "your@email.com"

When asked where to save the new key, hit enter to accept the default location.

Generating public/private rsa key pair.
Enter file in which to save the key (/Users/username/.ssh/id_rsa):

You will then be asked to provide an optional passphrase. This can be used to make your key even more secure, but if what you want is avoiding type your password every time you can skip it by hitting enter twice.

Enter passphrase (empty for no passphrase):
Enter same passphrase again:

When the key generation is complete, you should see the following confirmation:

Your identification has been saved in /Users/username/.ssh/id_rsa.
Your public key has been saved in /Users/username/.ssh/id_rsa.pub.
The key fingerprint is:
01:0f:f4:3b:ca:85:d6:17:a1:7d:f0:68:9d:f0:a2:db your@email.com
The key's randomart image is:
+--[ RSA 2048]----+
|                 |
|                 |
|        . E +    |
|       . o = .   |
|      . S =   o  |
|       o.O . o   |
|       o .+ .    |
|      . o+..     |
|       .+=o      |
+-----------------+

The random art image is an alternate way to match keys but we won’t be needing this.

Now you need to place a copy of your public key ony any servers you would like to use SSH to connect to, instead of logging in with a username and passwd.

Display the contents of your new public key file with cat:

$ cat ~/.ssh/id_rsa.pub

ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEA879BJGYlPTLIuc9/R5MYiN4yc/YiCLcdBpSdzgK9Dt0Bkfe3rSz5cPm4wmehdE7GkVFXrBJ2YHqPLuM1yx1AUxIebpwlIl9f/aUHOts9eVnVh4NztPy0iSU/Sv0b2ODQQvcy2vYcujlorscl8JjAgfWsO3W4iGEe6QwBpVomcME8IU35v5VbylM9ORQa6wvZMVrPECBvwItTY8cPWH3MGZiK/74eHbSLKA4PY3gM4GHI450Nie16yggEg2aTQfWA1rry9JYWEoHS9pJ1dnLqZU3k/8OWgqJrilwSoC5rGjgp93iu0H8T6+mEHGRQe84Nk1y5lESSWIbn6P636Bl3uQ== your@email.com

Copy the contents of the output.

$ ssh vlad@moon.euphoric.edu
Password: ********

Paste the content that you copy at the end of ~/.ssh/authorized_keys.

    moon> nano ~/.ssh/authorized_keys

After append the content, logout of the remote machine and try login again. If you setup your SSH key correctly you won’t need to type your password.

    moon> exit

$ ssh vlad@moon.euphoric.edu

SSH Files and Directories

The example of copying our public key to a remote machine, so that it can then be used when we next SSH into that remote machine, assumed that we already had a directory ~/.ssh/.

Whilst a remote server may support the use of SSH to login, your home directory there may not contain a .ssh directory by default.

We have already seen that we can use SSH to run commands on remote machines, so we can ensure that everything is set up as required before we place the copy of our public key on a remote machine.

Walking through this process allows us to highlight some of the typical requirements of the SSH protocol itself, as documented in the man-page for the ssh command.

Firstly, we check that we have a .ssh/ directory on another remote machine, comet

$ ssh vlad@comet "ls -ld ~/.ssh"
Password: ********

    ls: cannot access /home/vlad/.ssh: No such file or directory

Oh dear! We should create the directory; and check that it’s there (Note: two commands, seperated by a semicolon)

$ ssh vlad@comet "mkdir ~/.ssh; ls -ld ~/.ssh"
Password: ********

    drwxr-xr-x 2 vlad vlad 512 Jan 01 09:09 /home/vlad/.ssh

Now we have a dot-SSH directory, into which to place SSH-related files but we can see that the default permissions allow anyone to inspect the files within that directory.

For a protocol that is supposed to be secure, this is not considered a good thing and so the recommended permissions are read/write/execute for the user, and not accessible by others.

Let’s alter the permissions on the directory

$ ssh vlad@comet "chmod 700 ~/.ssh; ls -ld ~/.ssh"
Password: ********

    drwx------ 2 vlad vlad 512 Jan 01 09:09 /home/vlad/.ssh

That’s looks much better.

In the above example, it was suggested that we paste the content of our public key at the end of ~/.ssh/authorized_keys, however as we didn’t have a ~/.ssh/ on this remote machine, we can simply copy our public key over as the initial ~/.ssh/authorized_keys, and of course, we will use scp to do this, even though we don’t yet have passwordless SSH access set up.

$ scp ~/.ssh/id_rsa.pub vlad@comet:.ssh/authorized_keys
Password: ********

Note that the default target for the scp command on a remote machine is the home directory, so we have not needed to use the shorthand ~/.ssh/ or even the full path /home/vlad/.ssh/ to our home directory there.

Checking the permissions of the file we have just created on the remote machine, also serves to indicate that we no longer need to use our password, because we now have what’s needed to use SSH without it.

$ ssh vlad@comet "ls -l ~/.ssh"

    -rw-r--r-- 2 vlad vlad 512 Jan 01 09:11 /home/vlad/.ssh/authorized_keys

Whilst the authorized keys file is not considered to be highly sensitive, (after all, it contains public keys), we alter the permissions to match the man page’s recommendations

$ ssh vlad@comet "chmod go-r ~/.ssh/authorized_keys; ls -l ~/.ssh"

    -rw------- 2 vlad vlad 512 Jan 01 09:11 /home/vlad/.ssh/authorized_keys

Key Points

SSH is a secure alternative to username/password authorization

SSH keys are generated in public/private pairs. Your public key can be shared with others. The private keys stays on your machine only.

The ‘ssh’ and ‘scp’ utilities are secure alternatives to logging into, and copying files to/from remote machine

Permissions

Overview

Teaching: 10 min
Exercises: 0 min

Questions

Understanding file/directory permissions

Objectives

What are file/directory permissions?

How to view permissions?

How to change permissions?

File/directory permissions in Windows

Unix controls who can read, modify, and run files using permissions. We’ll discuss how Windows handles permissions at the end of the section: the concepts are similar, but the rules are different.

Let’s start with Nelle. She has a unique user name, nnemo, and a user ID, 1404.

Why Integer IDs?

Why integers for IDs? Again, the answer goes back to the early 1970s. Character strings like alan.turing are of varying length, and comparing one to another takes many instructions. Integers, on the other hand, use a fairly small amount of storage (typically four characters), and can be compared with a single instruction. To make operations fast and simple, programmers often keep track of things internally using integers, then use a lookup table of some kind to translate those integers into user-friendly text for presentation. Of course, programmers being programmers, they will often skip the user-friendly string part and just use the integers, in the same way that someone working in a lab might talk about Experiment 28 instead of “the chronotypical alpha-response trials on anacondas”.

Users can belong to any number of groups, each of which has a unique group name and numeric group ID. The list of who’s in what group is usually stored in the file /etc/group. (If you’re in front of a Unix machine right now, try running cat /etc/group to look at that file.)

Now let’s look at files and directories. Every file and directory on a Unix computer belongs to one owner and one group. Along with each file’s content, the operating system stores the numeric IDs of the user and group that own it.

The user-and-group model means that for each file every user on the system falls into one of three categories: the owner of the file, someone in the file’s group, and everyone else.

For each of these three categories, the computer keeps track of whether people in that category can read the file, write to the file, or execute the file (i.e., run it if it is a program).

For example, if a file had the following set of permissions:

	user	group	other
read	yes	yes	no
write	yes	no	no
execute	no	no	no

it would mean that:

the file’s owner can read and write it, but not run it;
other people in the file’s group can read it, but not modify it or run it; and
everybody else can do nothing with it at all.

Let’s look at this model in action. If we cd into the labs directory and run ls -F, it puts a * at the end of setup’s name. This is its way of telling us that setup is executable, i.e., that it’s (probably) something the computer can run.

$ cd labs
$ ls -F

safety.txt    setup*     waiver.txt

Necessary But Not Sufficient

The fact that something is marked as executable doesn’t actually mean it contains a program of some kind. We could easily mark this HTML file as executable using the commands that are introduced below. Depending on the operating system we’re using, trying to “run” it will either fail (because it doesn’t contain instructions the computer recognizes) or cause the operating system to open the file with whatever application usually handles it (such as a web browser).

Now let’s run the command ls -l:

$ ls -l

-rw-rw-r-- 1 vlad bio  1158  2010-07-11 08:22 safety.txt
-rwxr-xr-x 1 vlad bio 31988  2010-07-23 20:04 setup
-rw-rw-r-- 1 vlad bio  2312  2010-07-11 08:23 waiver.txt

The -l flag tells ls to give us a long-form listing. It’s a lot of information, so let’s go through the columns in turn.

On the right side, we have the files’ names. Next to them, moving left, are the times and dates they were last modified. Backup systems and other tools use this information in a variety of ways, but you can use it to tell when you (or anyone else with permission) last changed a file.

Next to the modification time is the file’s size in bytes and the names of the user and group that owns it (in this case, vlad and bio respectively). We’ll skip over the second column for now (the one showing 1 for each file) because it’s the first column that we care about most. This shows the file’s permissions, i.e., who can read, write, or execute it.

Let’s have a closer look at one of those permission strings: -rwxr-xr-x. The first character tells us what type of thing this is: - means it’s a regular file, while d means it’s a directory, and other characters mean more esoteric things.

The next three characters tell us what permissions the file’s owner has. Here, the owner can read, write, and execute the file: rwx. The middle triplet shows us the group’s permissions. If the permission is turned off, we see a dash, so r-x means “read and execute, but not write”. The final triplet shows us what everyone who isn’t the file’s owner, or in the file’s group, can do. In this case, it’s r-x again, so everyone on the system can look at the file’s contents and run it.

To change permissions, we use the chmod command (whose name stands for “change mode”). Here’s a long-form listing showing the permissions on the final grades in the course Vlad is teaching:

$ ls -l final.grd

-rwxrwxrwx 1 vlad bio  4215  2010-08-29 22:30 final.grd

Whoops: everyone in the world can read it—and what’s worse, modify it! (They could also try to run the grades file as a program, which would almost certainly not work.)

The command to change the owner’s permissions to rw- is:

$ chmod u=rw final.grd

The u signals that we’re changing the privileges of the user (i.e., the file’s owner), and rw is the new set of permissions. A quick ls -l shows us that it worked, because the owner’s permissions are now set to read and write:

$ ls -l final.grd

-rw-rwxrwx 1 vlad bio  4215  2010-08-30 08:19 final.grd

Let’s run chmod again to give the group read-only permission:

$ chmod g=r final.grd
$ ls -l final.grd

-rw-r--rw- 1 vlad bio  4215  2010-08-30 08:19 final.grd

And finally, let’s give “other” (everyone on the system who isn’t the file’s owner or in its group) no permissions at all:

$ chmod o= final.grd
$ ls -l final.grd

-rw-r----- 1 vlad bio  4215  2010-08-30 08:20 final.grd

Here, the o signals that we’re changing permissions for “other”, and since there’s nothing on the right of the =, “other”’s new permissions are empty.

We can search by permissions, too. Here, for example, we can use -type f -perm -u=x to find files that the user can execute:

$ find . -type f -perm -u=x

./tools/format
./tools/stats

Before we go any further, let’s run ls -a -l to get a long-form listing that includes directory entries that are normally hidden:

$ ls -a -l

drwxr-xr-x 1 vlad bio     0  2010-08-14 09:55 .
drwxr-xr-x 1 vlad bio  8192  2010-08-27 23:11 ..
-rw-rw-r-- 1 vlad bio  1158  2010-07-11 08:22 safety.txt
-rwxr-xr-x 1 vlad bio 31988  2010-07-23 20:04 setup
-rw-rw-r-- 1 vlad bio  2312  2010-07-11 08:23 waiver.txt

The permissions for . and .. (this directory and its parent) start with a d. But look at the rest of their permissions: the x means that “execute” is turned on. What does that mean? A directory isn’t a program—how can we “run” it?

In fact, x means something different for directories. It gives someone the right to traverse the directory, but not to look at its contents. The distinction is subtle, so let’s have a look at an example. Vlad’s home directory has three subdirectories called venus, mars, and pluto:

Execute Permission for Directories

Each of these has a subdirectory in turn called notes, and those sub-subdirectories contain various files. If a user’s permissions on venus are r-x, then if she tries to see the contents of venus and venus/notes using ls, the computer lets her see both. If her permissions on mars are just r--, then she is allowed to read the contents of both mars and mars/notes. But if her permissions on pluto are only --x, she cannot see what’s in the pluto directory: ls pluto will tell her she doesn’t have permission to view its contents. If she tries to look in pluto/notes, though, the computer will let her do that. She’s allowed to go through pluto, but not to look at what’s there. This trick gives people a way to make some of their directories visible to the world as a whole without opening up everything else.

What about Windows?

Those are the basics of permissions on Unix. As we said at the outset, though, things work differently on Windows. There, permissions are defined by access control lists, or ACLs. An ACL is a list of pairs, each of which combines a “who” with a “what”. For example, you could give the Mummy permission to append data to a file without giving him permission to read or delete it, and give Frankenstein permission to delete a file without being able to see what it contains.

This is more flexible that the Unix model, but it’s also more complex to administer and understand on small systems. (If you have a large computer system, nothing is easy to administer or understand.) Some modern variants of Unix support ACLs as well as the older read-write-execute permissions, but hardly anyone uses them.

Challenge

If ls -l myfile.php returns the following details:
-rwxr-xr-- 1 caro zoo  2312  2014-10-25 18:30 myfile.php
Which of the following statements is true?

caro (the owner) can read, write, and execute myfile.php

caro (the owner) cannot write to myfile.php

members of caro (a group) can read, write, and execute myfile.php

members of zoo (a group) cannot execute myfile.php

Solution

Option 1 is correct. The first triplet rwx indicates that the owner can read, write, and execute myfile.php. We know that caro is the owner because they are listed in the third column.

Option 2 is incorrect as we have just shown that caro can read, write, and execute myfile.php.

Option 3 is also incorrect because caro is not a group but an owner. The group that owns this file is zoo.

Option 4 is also incorrect because the second triplet r-x indicates that the group zoo can read and execute myfile.php.

Key Points

Correct permissions are critical for the security of a system.

File permissions describe who and what can read, write, modify, and access a file.

Use ls -l to view the permissions for a specific file.

Use chmod to change permissions on a file or directory.

Job control

Overview

Teaching: 5 min
Exercises: 0 min

Questions

How do keep track of the process running on my machine?

Can I run more than one program/script from within a shell?

Objectives

Learn how to use ps to get information about the state of processes

Learn how to control, ie., “stop/pause/background/foreground” processes

The shell-novice lesson explained how we run programs or scripts from the shell’s command line.

We’ll now take a look at how to control programs once they’re running. This is called job control, and while it’s less important today than it was back in the Dark Ages, it is coming back into its own as more people begin to leverage the power of computer networks.

When we talk about controlling programs, what we really mean is controlling processes. As we said earlier, a process is just a program that’s in memory and executing. Some of the processes on your computer are yours: they’re running programs you explicitly asked for, like your web browser. Many others belong to the operating system that manages your computer for you, or, if you’re on a shared machine, to other users.

The `ps` command

You can use the ps command to list processes, just as you use ls to list files and directories.

Behaviour of the ps command

The ps command has a swathe of option flags that control its behaviour and, what’s more, the sets of flags and default behaviour vary across different platforms.

A bare invocation of ps only shows you basic information about your, active processes.

After that, this is a command that it is worth reading the ‘man page’ for.

$ ps

  PID TTY          TIME CMD
12767 pts/0    00:00:00 bash
15283 pts/0    00:00:00 ps

At the time you ran the ps command, you had two active processes, your (bash) shell and the (ps) command you had invoked in it.

Chances are that you were aware of that information, without needing to run a command to tell you it, so let’s try and put some flesh on that bare bones information.

$ ps -f

UID        PID  PPID  C STIME TTY          TIME CMD
vlad     12396 25397  0 14:28 pts/0    00:00:00 ps -f
vlad     25397 25396  0 12:49 pts/0    00:01:39 bash

In case you haven’t had time to do a man ps yet, be aware that the -f flag doesn’t stand for “flesh on the bones” but for “Do full-format listing”, although even then, there are “fuller” versions of the ps output.

But what are we being told here?

Every process has a unique process id (PID). Remember, this is a property of the process, not of the program that process is executing: if you are running three instances of your browser at once, each will have its own process ID.

The third column in this listing, PPID, shows the ID of each process’s parent. Every process on a computer is spawned by another, which is its parent (except, of course, for the bootstrap process that runs automatically when the computer starts up).

Clearly, the ps -f that was run is a child process of the (bash) shell it was invoked in.

Column 1 shows the username of the user the processes are being run by. This is the username the computer uses when checking permissions: each process is allowed to access exactly the same things as the user running it, no more, no less.

Column 5, STIME, shows when the process started running, whilst Column 7, TIME, shows you how much time the process has used, whilst Column 8, CMD, shows what program the process is executing.

Column 6, TTY, shows the ID of the terminal this process is running in. Once upon a time, this really would have been a terminal connected to a central timeshared computer. It isn’t as important these days, except that if a process is a system service, such as a network monitor, ps will display a question mark for its terminal, since it doesn’t actually have one.

The fourth column, C, is an indication of the percentage of processor (CPU) utilization.

Your version of ps may show more or fewer columns, or may show them in a different order, but the same information is generally available everywhere, and the column headers are generally consistent.

Stopping, pausing, resuming, and backgrounding, processes

The shell provides several commands for stopping, pausing, and resuming processes. To see them in action, let’s run our analyze program on our latest data files. After a few minutes go by, we realize that this is going to take a while to finish. Being impatient, we kill the process by pressing Control-C. This stops the currently-executing program right away. Any results it had calculated, but not written to disk, are lost.

$ ./analyze results*.dat

...a few minutes pass...
^C

Let’s run that same command again, with an ampersand & at the end of the line to tell the shell we want it to run in the background:

$ ./analyze results*.dat &

When we do this, the shell launches the program as before. Instead of leaving our keyboard and screen connected to the program’s standard input and output, though, the shell hangs onto them. This means the shell can give us a fresh command prompt, and start running other commands, right away. Here, for example, we’re putting some parameters for the next run of the program in a file:

$ cat > params.txt
density: 22.0
viscosity: 0.75
^D

(Remember, ^D is the shell’s way of showing Control-D, which means “end of input”.) Now let’s run the jobs command, which tells us what processes are currently running in the background:

$ jobs

[1] ./analyze results01.dat results02.dat results03.dat

Since we’re about to go and get coffee, we might as well use the foreground command, fg, to bring our background job into the foreground:

$ fg

...a few minutes pass...

When analyze finishes running, the shell gives us a fresh prompt as usual. If we had several jobs running in the background, we could control which one we brought to the foreground using fg %1, fg %2, and so on. The IDs are not the process IDs. Instead, they are the job IDs displayed by the jobs command.

The shell gives us one more tool for job control: if a process is already running in the foreground, Control-Z will pause it and return control to the shell. We can then use fg to resume it in the foreground, or bg to resume it as a background job. For example, let’s run analyze again, and then press Control-Z. The shell immediately tells us that our program has been stopped, and gives us its job number:

$ ./analyze results01.dat
^Z

[1]  Stopped   ./analyze results01.dat

If we type bg %1, the shell starts the process running again, but in the background. We can check that it’s running using jobs, and kill it while it’s still in the background using kill and the job number. This has the same effect as bringing it to the foreground and then pressing Control-C:

$ bg %1

$ jobs

[1] ./analyze results01.dat

$ kill %1

Job control was important when users only had one terminal window at a time. It’s less important now: if we want to run another program, it’s easy enough to open another window and run it there. However, these ideas and tools are making a comeback, as they’re often the easiest way to run and control programs on remote computers elsewhere on the network. This lesson’s ssh episode has more to say about that.

Key Points

When we talk of ‘job control’, we really mean ‘process control’

A running process can be stopped, paused, and/or made to run in the background

A process can be started so as to immediately run in the background

Paused or backgrounded processes can be brought back into the foreground

Process information can be inspected with ps

Unix Shell

Course Logistics and Getting to know people

Overview

Using Software Carpentry

Zoom and Slack

Key Points

Introducing the Shell

Overview

Background

The Shell

Command not found

Nelle’s Pipeline: A Typical Problem

Key Points

Navigating Files and Directories

Overview

Home Directory Variation

Slashes

Clearing your terminal

Getting help

The --help option

Unsupported command-line options

The man command

Manual pages on the web

Exploring More ls Flags

Solution

Listing in Reverse Chronological Order

Solution

Exploring Other Directories

Other Hidden Files

Two More Shortcuts

Absolute vs Relative Paths

Solution

Relative Path Resolution

Solution

ls Reading Comprehension

Solution

General Syntax of a Shell Command

Nelle’s Pipeline: Organizing Files

Key Points

BREAK

Overview

Key Points

Working With Files and Directories

Overview

Creating directories

Step one: see where we are and what we already have

Create a directory

Two ways of doing the same thing

Good names for files and directories

Create a text file

Which Editor?

Control, Ctrl, or ^ Key

Meta Key

Creating Files a Different Way

Solution

What’s In A Name?

Moving files and directories

Moving Files to a new folder

Solution

Copying files and directories

Renaming Files

Solution

Moving and Copying

Solution

Removing files and directories

Deleting Is Forever

Using rm Safely

Solution

Operations with multiple files and directories

Copy with Multiple Filenames

Solution

Using wildcards for accessing multiple files at once

Wildcards

List filenames matching a pattern

Solution

More on Wildcards

Solution

Organizing Directories and Files

Solution

Reproduce a folder structure

The `--help` option

The `man` command

Exploring More `ls` Flags

`ls` Reading Comprehension

Using `rm` Safely

What Does `sort -n` Do?

What Does `>>` Mean?