Introducing the Shell

Written by J. Kitzes, Edited by M. Wilber

Our introduction to best practices in scientific computing begins with one of the oldest and most venerable software tools - the shell. As with every tool and practice that we'll cover during this two day workshop, we'll only have time to introduce you to the very basics of using the shell. We'll focus our time here on (a) the core skills that you'll need to get stuff done, including in particular those that you'll need to complete the lessons in the rest of the workshop, and (b) the overarching concepts of scientific computing that the use of the shell illustrates.

Before we get started, I'll note that some of you, especially those of you who deal routinely with large numbers of small files (i.e., sensor data saved every hour by an instrument), will benefit from learning more advanced skills than those that we'll cover here. If you're interested, check out this lengthier and more detailed shell tutorial.

So, to kick off, what exactly is "the shell"? Although these days when we think of "a computer" we immediately imagine buttons, menus, a mouse, etc., you're probably aware that this wasn't always the case. In the days before graphical user interfaces (GUIs), all interaction with computers occurred through a process that involved sending a computer text commands and waiting for the computer to show you some text back in response. Today, this text-based manner of interacting with a computer is known as a command line interface, and using it is known as "working at the command line".

When we're working at the command line, our interactions with the computer follow what's known as a read-evaluate-print loop, which means that we type in something, the computer reads it, does something that we've told it to do, and prints the output back to us. We do this over and over again until we're done and log off. Although we've used the word "computer" above to indicate the actor who reads and replies to our text input, the actor that we are communicating with directly is actually a specialized program called "the shell". We can tell the shell to do all sorts of things, including to work with files on our hard drive and to run other specialized command line programs.

Since this is the 2010's, why should we bother learning how to use the shell? The most important reason is that much of the rest of the scientific computing pipeline depends on it. Once you break out of your comfortable R GUI and start trying to practice more advanced scientific computing, you'll immediately need to interact with the shell. On an immediate basis, you'll need to be comfortable with the skills in this lesson in order to complete our subsequent lessons on scientific programming, particularly version control. Furthermore, once you become comfortable in the shell, you'll find that there are many tasks that you can do more quickly through the shell than through your old graphical programs.

More specifically, in this lesson we'll review how to use the shell for four common types of tasks that are a part of scientific computing.

Viewing and interacting with files and directories on your hard drive
Launching and using command line programs
Chaining different programs together to achieve overall computing tasks
Searching for text within files

Launching the shell

To get started, let's launch a shell session. If you're on a Mac, go to your Applications folder, then to the folder Utilities, then open the program Terminal. On Windows, presuming that you've installed mysysgit as per the instructions, you should have a desktop shortcut and/or a shortcut in your Programs menu to open mysysgit. If you're running Linux, you probably already know where the shell is and how to use it - if you're running our Linux Virtual Machine for the first time, look under the button at the bottom left of the screen (that looks like the old Windows Start Menu) for something called shell or terminal.

Once you open the Terminal program, which runs the shell program for us, you'll see a blank window with something like this printed in it.

Last login: Wed Mar 25 10:57:31 on ttys009
~$

This means you're set to go, even if you don't exactly know where we're going yet. You may have other text in front of the $ symbol on your computer, which is fine. You'll notice that if you start typing, your text appears following the $ symbol. This state is known as being at a command prompt, and it's the first step in the read-execute-print loop that we mentioned earlier. In other words, the shell is now waiting for us to tell it to do something.

Working with directories and files

Probably the most fundamental and most frequent type of task that you'll complete in the shell will involve navigating around your hard drive and working with files and directories. Head back to the shell and to your command prompt, type the command pwd and hit return, and watch what the shell prints out.

~$ pwd
/Users/mqwilber

The response of your shell will be different, of course, unless your name is also Mark Wilber. The command pwd is short for "print working directory" and it tells us which directory the shell is currently in. (This is the command line equivalent to opening a particular folder on your hard drive.) When you launch a shell session, you're automatically placed in a location known as your "home directory" to start off.

So now we know what directory we're in, but we don't know what's in it. To see the contents of this folder, type the command ls, short for "listing", and hit return.

~$ ls
Applications   Downloads   Movies      Pictures    Websites
Desktop        Dropbox     Music       Public      anaconda
Documents      Library     Packages    Repos

Once again, you'll see something different depending on what's actually in this folder on your computer. If you want to confirm that you know what's going on, use your "normal" graphical operating system to open the folder indicated by the pwd command, and you'll see that these folders and/or files are, in fact, where the shell says they are.

Now that we know what directory ("folder", in a graphical interface) we're in and what's in this directory, let's start moving around our file system. To do this, we use a command cd, for "change directory".

~$ cd
~$

Hmm, that didn't seem to do anything. It turns out that running the command cd without any additional information changes your working directory to your home directory, which is where we already are (since the shell places us in our home directory by default). To be useful, we need to give cd an argument, which is some information following the name of the command itself. The first argument that you give cd is an indication of which directory you'd like to go to.

We know from running ls that one of the subdirectories of your home directory is "Desktop" (hopefully this is true regardless of what computer or virtual machine you're running - if this is not true, ask one of the helpers or instructors for assistance). Let's change directories into our Desktop directory.

~$ cd Desktop
Desktop$

If you run the command ls, you should now see a list of all of the files and folders on your computer's desktop. If ls prints no output, then you have no files or folders currently sitting on your desktop - congrats on being organized!

Quick tip - now that we're in the Desktop directory, how to we go back "up" to our home directory. For that we can use the special argument .. to the cd command.

Desktop$ cd ..
~$ pwd
/Users/mqwilber
~$ cd Desktop/
Desktop$ pwd
/Users/mqwilber/Desktop
Desktop$

Before we move on to working with files, one final important vocabulary word is "path". The path refers to the location of a directory or file on your hard drive - we would thus say that /Users/mqwilber/Desktop is the path to my Desktop directory. There are two ways to think of paths - absolute and relative. Absolute paths, like /Users/mqwilber/Desktop, give the location of a file or directory from the root of your entire file system, which is indicated by the leading / character (cd / will take you to this root). Relative paths specify the location of a file or folder relative to your present working directory (i.e., the relative path is "glued on" to your current path). If you're in your home folder /Users/mqwilber, the commands cd /Users/mqwilber/Desktop and cd Desktop thus take you to the same place, but the former uses an absolute path (and would work from anywhere) while the latter uses a relative path.

Finally, remember that if you ever get lost, cd with no arguments will take you back to your home folder.

Now that you're in your Desktop directory, let's create a directory to hold all of the materials for this workshop. The command mkdir, short for "make directory", will create a directory. It requires one argument, which is the path (absolute or relative) to the directory that you wish to create.

Desktop$ mkdir workshop
Desktop$ cd workshop
workshop$

We've now created and moved into a directory named workshop in our Desktop directory. If you look at your actual Desktop on your computer, you should see that, in fact, a new folder called workshop has appeared there.

Now that we've created our directory, let's put a file in it. A simple command that lets us create an empty file with nothing in it is touch, which takes one argument for the path to the file (using the file name as the argument represents a relative path, which puts the file in your current directory).

workshop$ touch file.txt
workshop$ ls
file.txt

We can easily rename or move existing files with the mv command, which takes one argument for the existing path to the file and one argument for the new path to the file. The command below uses two relative paths to perform a simple rename of the file.

workshop$ mv file.txt file1.txt
workshop$ ls
file1.txt

Since this file isn't doing much for us, let's delete it using rm, short for "remove".

workshop$ rm file1.txt
workshop$ ls
workshop$

Important note - the shell has no concept of a trash can, so once you've deleted a file using rm, it's gone forever. As such, use it carefully.

Removing an empty directory is just as easy as removing a file, but removing a full directory requires us to add one extra argument to the rm command (more on this concept later) - rm -r directory-name will delete a directory called directory-name and all of its contents.

Exercise 1

Change directories to your desktop. Use touch to recreate file.txt on your Desktop, and then use mv to move it into your workshop directory. Remove the workshop directory and the file in it. Recreate the workshop directory and cd back into it.

As you perform the above steps, there are two very useful productivity shortcuts for working in the shell that you should try out. The first is called tab completion. After you create the workshop directory, for example, try typing cd wo and then hitting tab - you'll see that the shell fills in the rest of the directory or file name for you (if there are multiple options that start with those letters, your shell will either show you all of the options or do nothing - in either case, you'll need to enter more letters and press tab again). The second is the use of the up arrow, which will scroll through all of your previous shell commands - once you find one that you like, you can hit return to execute it again.

A final tip on naming files and directories. Although modern shells try hard to accommodate special characters like spaces in file and directory names, these will sometimes (even often) cause trouble for your command line work. It's highly recommended that you use only regular letters, numbers, and dash and underscore symbols in your file names to prevent any trouble later on.

Running command line programs

Now that we've discussed using the shell to navigate our file system, we'll move on to discussing the idea of executing command line programs from the shell. In the same way that you have graphical applications on your computer that you can run with a double click, your computer comes bundled with many command line programs that you can run by typing their names into the shell. Some of these will simply take an input and spit out an output, while some of them will drop you into an entirely new environment specific to that program. We'll examine both of these in turn.

The first kind of command line program are those that print their results right to the terminal in front of you. In face, we've sneakily already seen several of these - it turns out that the various commands that we used in the last section are actually programs that are executed by the shell. If you want to see where these programs are saved on your hard drive (sort of like the command line equivalent of the Applications or Programs folder that you're used to), use the command (excuse me, the program) which.

~$ which ls
/bin/ls

This tells you that the program ls actual resides in a directory called bin that is found in the root folder of your file system. You've probably never gone there, and in fact most graphical operating systems will try to hide folders like this from you so that you don't do something dangerous. You can easily cd into those folders and list their contents from the shell, if you're curious, and with enough work you can also view them from your normal graphical operating system (on a Mac, for example, go to Finder, the Go menu, and Go To Folder, then type in this path).

As we saw earlier, command line programs take two additional types of input, known as arguments and options (or flags). Arguments are the words that you type after the program name (touch file.txt, cd Desktop) and usually tell the program what file or directory it should perform its operations on. Options always start with a dash or two dashes and are used to modify how the program operates. For example, try running the ls command with the option -l. Sometimes options can themselves have arguments, so that you have the program name, the arguments, the options, and the options to the arguments.

Other than asking an instructor (which will not be easy three days from now), how do you know what arguments and options are available for each program? In most shell sessions (this may not work on Windows with mysysgit), you can type the command man followed by the name of the program, and you will be shown the help file for that command, which will list all of the available arguments and options. Use the arrow keys to scroll up and down, and type q to quit when you're done.

Aside from programs like ls that print their output right to the command line (in technical terms, they print to "standard output"), there are also programs that launch entire environments for themselves. One of those is the command line text editor nano. First, make sure that you're in your workshop directory, then execute the command nano.

When you do this, your shell session will appear to vanish (don't worry, it's still there in the background), and you'll be dropped into a very simple text editor. Enter the following lines in your text editor.

Fox,1
Wolverine,5
Wolf,3

When you're done, as helpfully suggested by the lines at the bottom of your window, hit Ctrl-x to exit (the ^ symbol is shorthand for the Control key). It will ask you if you want to save the file - type Y for yes. Name the file mammals.csv and hit return. You'll now be back in your shell session - run ls and you'll see that you've created a new csv file in this directory.

Exercise 2

Create another file in this directory called birds.csv that indicates that you saw 4 Owl, 3 Tern, and 7 Hawk (use the same format as the mammals.csv file to enter this data).

You may recognize the file extension csv as standing for "comma separated values", and you've probably opened csv files before in a spreadsheet program such as Excel. As suggested by the above, csv files are actually nothing more than plain text files in which the "columns" of data are separated by commas. As plain text files, command line programs (including version control software) can do a lot of useful things with csv files, making them a good alternative to Excel file formats for saving and working with tabular data.

Exercise 3

There are a few ways to easily view plain text files from the command line. Try using the programs cat and less to view your mammals.csv file. Can you see that one of these prints to standard out and one drops you into its own environment? (For the latter, press q to exit when you're done.)

R, the program/language that we will be using during this workshop can also be invoked from the command line (Note: This will not work for Windows users). Just type R (or r) with no arguments at the command prompt and you should see

 ~$ R

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

Although your shell session has seemingly not vanished in the same way as it did when you opened nano, you'll notice that your command prompt at the bottom of the screen now starts with > symbols instead of $. This helpfully indicates to you that you're actually inside of the R console, not the shell, at this point, and that whatever you type will be executed by R. Try typing pwd and hitting return, for example, and notice that R has no idea what you're talking about. Instead, try typing getwd() (meaning get working directory; the equivalent of pwd) and notice that R now tells you where you are.

As another example, type 2+2 and hit return, though, and you'll see that R knows what to do with that. To quit, type q() and then y press return, and you'll see that the $ prompt indicates that you're now back in the shell. While we often don't interact with R directly through the command line, it is important to know that you can!

Chaining commands

You may have noticed (or inferred) that there are a whole lot of command line programs available to us, and that each of them performs a fairly narrow, specific task. This is one of the basic philosophies of the Unix operating system (where most of these command line programs originated) - have lots of small pieces, each of which do their job very well, that can be combined to create larger "pipelines" that perform more complex analyses. This is a perspective that will also be at the heart of our later discussions of structuring scientific programs. In this section, we'll look at two basic techniques for combining programs and working with their output, known as redirects and pipes.

The first of these techniques, a redirect, is most commonly used to "redirect" the output that a program would normally print to your terminal window into a file. For example, the cat command, which we saw above, will print the contents of a file (or multiple files, glued together) to the terminal window.

workshop$ cat mammals.csv birds.csv
Fox,1
Wolverine,5
Wolf,3
Owl,4
Tern,3
Hawk,7

Let's say that we want to create a combined csv file animals.csv that contains both the mammal and the bird data. To do this, we can save the output of our cat command above to a file by using the > character, as shown below.

workshop$ cat mammals.csv birds.csv > animals.csv
workshop$ ls
animals.csv	birds.csv	mammals.csv
workshop$ cat animals.csv 
Fox,1
Wolverine,5
Wolf,3
Owl,4
Tern,3
Hawk,7

While the redirect symbol > will create a new file, overwriting an old one if it exists, using >> will instead append the output to a file if it already exists.

A second technique, a pipe, is used to turn the output of one program into the input for another program. Let's say that we not only wanted to combine the mammal and bird tables, but we also wanted to sort the resulting combined table by animal name. For sorting, we can use the command sort, which prints the sorted contents of a file to the terminal.

workshop$ sort animals.csv
Fox,1
Hawk,7
Owl,4
Tern,3
Wolf,3
Wolverine,5
workshop$ sort animals.csv > sorted_animals.csv

Note how the output of sort animals.csv compares to the output of cat animals.csv. The second command here saves our sorted list to a new csv file.

Conceptually, we can see that what we've done is use cat to combine our two files, then take the result of that combination and give it to the sort command, then take the output of sort and save it to a file. The first two of these steps involves taking the output of one command and giving it to another, which here we've done by saving the intermediate file animals.csv. We can skip that step by using a pipe.

workshop$ rm animals.csv sorted_animals.csv
workshop$ cat mammals.csv birds.csv | sort > sorted_animals.csv
workshop$ cat sorted_animals.csv 
Fox,1
Hawk,7
Owl,4
Tern,3
Wolf,3
Wolverine,5

Here we first removed animals.csv and sorted_animals.csv from our previous commands. Then we ran the cat command on our two files, piped the output of that command directly to sort, and redirected that output directly to our file sorted_animals.csv.

Exercise 4

The command wc counts the number of lines, words, and bytes in a file. Combine the command wc with the above pipe/redirect command to instead save a text file, n_records.txt, that contains a single number giving the number of total records of both mammal and bird sightings (of which there are 6). (Hint: See the man page for wc for an option to return just the line count.)

Finding things

We'll close our quick tour of the shell by discussing how to use a well-known command line program, grepto find lines within files that match a pattern. Although grep is only one of many searching tools that you might use, it is very widely known, relatively simple to learn, and will give us the opportunity to briefly examine the topic of "regular expressions".

The basic usage of grep involves two arguments, the first giving the string to match and the second giving the file to match it in. For example, if we wanted to find all of the animals with 3 sightings, we could run

workshop$ grep 3 sorted_animals.csv
Tern,3
Wolf,3

Since grep matches text strings, independent of their locations within lines, we can also easily search, for example, for all lines containing the letter "n".

workshop$ grep n sorted_animals.csv
Tern,3
Wolverine,5

grep has lots of flags that change its behavior, and I encourage you to review these using man grep (or grep --help in Git Bash). For example, -n will print the number line for each match and -i makes the search insensitive to case.

workshop$ grep -n o sorted_animals.csv
1:Fox,1
5:Wolf,3
6:Wolverine,5
workshop$ grep -n -i o sorted_animals.csv
1:Fox,1
3:Owl,4
5:Wolf,3
6:Wolverine,5

The real power of grep, however, comes from its ability to use a special language, known as regular expressions, to specify the search patterns. This allows us to include wildcards in our searches, and to search for more complex patterns than just consecutive letters. Regular expressions are a whole lesson unto themselves, but here are a few quick tips:

^ stands for the start of a line, and $ for the end of a line
. stands for any character
* means to match any number of the previous character, so .*, for example, matches any number of any character
[] matches any one of the characters between the brackets

To use regular expressions in our grep calls, we use the option -E to denote that we're using extended regular expression as our pattern. For example, here's an expression to find all lines that start with the letter "W"

workshop$ grep -E '^W' sorted_animals.csv
Wolf,3
Wolverine,5

and one to find all the lines in which the second letter is "o".

workshop$ grep -E '^.o' sorted_animals.csv
Fox,1
Wolf,3
Wolverine,5

Exercise 6

Using regular search strings or regular expressions where necessary, use grep to extract lines from `sorted_animals.csv for which (1) the second letter is a vowel (all animals except Owl), and (2) the line contains an "r" and later an "n" (Tern and Wolverine).

It's usually the case in practice that we'll combine grep with pipes and redirects to immediately do additional processing on the results of our search. That said, a very simple and common use case is grep TODO *.R, which searches for and prints all of the lines (usually code comments) containing the string TODO that occur in all of the R files in this directory (the *.R uses a simple system wildcard to find all files ending with .R in this directory).

One final note about wildcards - unfortunately, there are several possible "languages" for using wildcards that you may encounter, and they are not consistent with each other. The other most widely used wildcard syntax is known as globbing, and it's what's used by the bash shell by default. The most important difference is the * symbol, which in "regular" shell commands is used to represent any number of characters (like .* in a regular expression). So ls *.jpg, for example, will list all of the JPG files in a directory, cat a*.csv will print the contents of all csv files starting with the letter "a" in a directory, and mv *rd* /subdir will move all files containing "rd" into subdir.

Wrapping up

Now that you're expert beginner shell users, here's a final exercise to integrate all that we've learned so far.

Exercise 5

cd to your desktop and create a directory called classes.

Using nano, create two text files in this directory, fall.txt and spring.txt, which contain one line for the title and units of each class that you took (or wanted to take) last fall and that you took/are taking this spring/winter. For example, Quantitative Bio (3). If you can't remember or didn't take any, just make some up!

Using pipes, redirects, and/or the programs that we've mentioned so far, save a file 3_unit_classes.txt that contains a single number giving the count of the number of classes you will take this year that are exactly 3 units (or some other unit count, if you didn't take any 3 unit classes).