Part 1: Review of some basics

Owned by Anna Battenhouse
Last updated: Nov 05, 2024

Commands, options, arguments & command line input

The Intro Unix: The Bash shell and commands section introduced the bash  REPL – a Read, Eval, Print Loop that processes lines of command input. To review, a command consists of:

  • The command name – any built-in Linux/Unix commands, or the name of a 3rd party program or user-written script
  • One or more (optional) options, usually noted with a leading dash ( - ) or double-dash ( -- ).
  • One or more command-line arguments, which are often (but not always) file names

The shell executes its REPL when it sees a linefeed (a.k.a newline), which happens when you press Enter after typing the command.

Command options

Types of command options:

  • Short (1-character) options which can be provided separately, prefixed by a single dash ( - )
    • or can be combined with the combination prefixed by a single dash (e.g. ls -lah)
  • Long (multi-character/"word") options are prefixed with a double dash ( -- ) and must be supplied separately.
  • Many utilities have equivalent long and short options, both of which can have values.
    • The short option and its value are usually separated by a space, but can also be run together (e.g. -f 2 or -f2)
    • Strictly speaking, the long option and its value should be separated by an equal sign (=) according to the POSIX standard (see https://en.wikipedia.org/wiki/POSIX). But many programs let you use a space as separator also.
  • Options usually come before arguments, but may also be allowed after the arguments depending on the tool.

More at: Intro Unix: The Bash shell and commands: Command options

Getting help

To learn what options and arguments a command has:

  1. In the Terminal, type in the command name then the --help long option (e.g. ls --help)
    • Works for most Linux commands
      • 3rd party tools may use -h or -? or even /? instead
    • May produce a lot of output, so you may need to scroll up quite a bit or pipe the output to a pager
      • e.g. ls --help | more
  2. Use the built-in manual system (e.g. type man ls)
    • This system uses the less pager (space advances the output by one screen/"page"; typing q exits the display)
  3. Ask the Google, e.g. search for ls man page
    • Can be easier to read
  4. Consult our Intro Unix: Some Linux commands wiki page
    • It lists many useful Linux commands along with some of their commonly used options

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Literal characters and metacharacters

In the bash shell, and in most tools and programming environment, there are two kinds of input:

  • literal characters, that just represent (and print as) themselves
    • e.g. alphanumeric characters A-Z, a-z, 0-9
  • metacharacters - these are special characters that are associated with an operation in the environment
    • e.g. the Enter key that ends the current line

There are many metacharacters in bash:  # \ $ | ~ [ ] " ` ' { }  to name a few.

We'll be emphasizing the different metacharacters and their usages – which can depend on the context where they're used – both in the bash command line and in commands/programs called from bash.

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Command line history and editing

Sometimes you want to repeat a command you've entered before, possibly with some changes.

  • The built-in history command lists the commands you've entered, each with a number.
    • You can re-execute any command in the history by typing an exclamation point ( ! ) then the number
    • e.g. !15 re-executes the 15th command in your history.
    • Only commands in your current bash session are in the history, but you can always save them for future reference, e.g. history > ~/history.2024-11-08.
  • Use Up arrow to retrieve any of the last 50+ commands you've typed, going backwards through your history.
    • You can then edit the retrieved line, and hit Enter (even in the middle of the command), and the shell will use that command.
  • The Down arrow "scrolls" forward from where you are in the command history.

For how to edit text on the command line, see: Intro Unix: The Bash shell and commands: Command line history and editing

Tab key completion

Hitting Tab when entering command line text invokes shell completion, instructing the shell to try to guess what you're doing and finish the typing for you. It's almost magic!

On most modern Linux shells you use Tab completion by pressing:

  • single Tab – completes file or directory name up to any ambiguous part
    • if nothing shows up, there is no unambiguous match
  • Tab twice – display all possible completions
    • you then decide where to go next

Let's have some fun with our friend the Tab key. Follow along if you can, as we use the Tab key to see the /stor/work/CBRS_unix/fastq path.

ls /st                     # press Tab key - expands to /stor/ which is the only match
ls /stor/w                 # press Tab key again - expands to /stor/work/, again the only match
ls /stor/work/C            # press Tab once - nothing happens because there are multiple matches
ls /stor/work/C            # press Tab a 2nd time - all matching directories listed
ls /stor/work/CB           # press Tab key - expands to /stor/work/CBRS_unix
ls /stor/work/CBRS_unix    # press Tab twice to see all completions
ls /stor/work/CBRS_unix/f  # press Tab once - expands to /stor/work/CBRS_unix/fastq

Tab key completion also works on commands! Type "bowtie" and Tab twice to see all the programs in the bowtie2 and bowtie tool suites.

Basic text manipulation

Standard streams and piping

A key to text manipulation is understanding Unix streams, which represent flows of characters. Every Unix program has three "built-in" streams: standard input, standard output and standard error. 

Most programs/commands read input data from some source, then write output to some destination. A data source can be a file, but can also be standard input. Similarly, a data destination can be a file but can also be a stream such as standard output.

The power of the Linux command line is due in no small part to the power of piping. The pipe operator ( | ) connects one program's standard output to the next program's standard input.

The key to the power of piping is that most Unix commands can accept input from standard input instead of from files. So, for example, these two expressions appear equivalent:

more jabberwocky.txt
cat jabberwocky.txt | more

The main differences between these two commands:

  • In more jaberwocky.txt, it is the more command that reads the file and performs its operations
    • displays some data on standard output, waits for a space on standard input, repeat until no more file data
    • since more is reading the file, it can display progress information about how much data has been read
  • In cat jabberwocky.txt | more, the cat program reads the file data and writes it to its standard output.
    • the pipe operator ( | ) then connects the standard output from cat to standard input of the more command
    • the more command then reads its input from standard input, instead of from a file
      • and causes the cat program to block – stop writing data to its standard output until requested
    • more displays some data on standard output, waits for a space on standard input, then requests more input
      • repeat until no more data from cat.
    • since the data coming in to more is from an anonymous pipe, more cannot display progress information

More at: Intro Unix: Viewing text in files: Standard streams and piping

echo, head, tail, cat -n, wc

The head and tail commands can be used to view/extract specific parts of large files.

  • With no options, head shows the first 10 lines of its input and tail shows the last 10 lines.
    • You can use the -n option to specify how many lines to view, or just put the number you want after a dash (e.g. head -5 for 5 lines or head -1 for 1 line).
  • To start viewing lines at a particular line number, use tail and put a plus sign (+) in front of the number (with or without the -n option).
  • The cat -n option adds line numbers to the text it displays, which can help orient you when dealing with large files

Use the wc (word count) command to count text lines (wc -l) or characters (wc -c).

echo is the bash command to output text.

  • echo -e says to enable interpretation of backslash escapes
    • so, for example, \n is interpreted as a linefeed, and \t as a tab character
  • echo -n says don't output the trailing newline (linefeed) character

Examples:

head -n 5 haiku.txt                      # display the 1st 5 lines of "haiku.txt"  
cat -n haiku.txt                         # display "haiku.txt" contents with line numbers        
cat -n haiku.txt | tail -n 7             # display the last 7 lines of "haiku.txt"
cat -n haiku.txt | tail -n +7            # display text in "haiku.txt" starting at line 7
cat -n haiku.txt | tail -n +5 | head -3  # display the middle stanza of "haiku.txt"

wc -l haiku.txt                          # count lines in "haiku.txt" file
cat haiku.txt | wc -l                    # use wc -l to count lines of piped-in text

echo 'Hello world!' | wc -c              # count characters output by echo, including the trailing newline
echo -n 'Hello world' ! wc -c            # count characters output by echo, without the trailing newline

echo -e "aa\nbb\ncc"                     # output 3 lines of text using \n to represent newlines

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Other shell concepts

Environment variables

Environment variables are just like variables in a programming language (in fact bash is a complete programming language): they are names that hold a value assigned to them. As with all programming language variables, they have two operations:

  1. variable definition - assign a value to a variable name
  2. variable reference - use the variable name to represent the value it holds

In bash, you define (set/assign) an environment variable like this:

# Assign the environment variable named "varname" the value "hello world!"
varname='hello world!'
  • Do not put spaces around the equals sign when assigning environment variable values! The shell is very picky about this.
  • Always enclose environment variable values that contain spaces in single or double quotes (see below)
  • Variable names can only contain alphnumeric (A-Z, a-z, 0-9) and underscore ( _ ) characters, and must begin with a letter.

An environment variable can be referenced by putting the dollar sign ( $ ) metacharacter in front of the variable name (e.g $varname) or the slightly longer syntax: ${varname}.

Examples:

foo="My USER name is $USER";  echo $foo   # The variable "$USER" is evaluated and its value substituted
foo="My USER name is ${USER}; echo $foo   # Same as above using longer evaluation syntax

# Undefined environment variables just appear as empty text
bar='chess'; echo "Today's game is: $bar"
unset bar;   echo "Today's game is: $bar"

# Evaluating an environment variable that contains an underscore 
# may need to use the longer evaluation syntax, if the literal text
# before or after it is an underscore.
my_var="middle"
echo "File name is: foo_${my_var}_bar.txt"

Your built-in environment variables (e.g. $USER, $MY_GROUP, $PATH) and their values can be viewed with the env command.

More at: Intro Unix: Writing text: Environment variables

Quoting in the shell

When the shell processes a command line, it first parses the text into tokens ("words"), which are groups of characters separated by whitespace (one or more space characters). Quoting affects how this parsing happens, including how metacharacters are treated and how text is grouped.

There are three types of quoting in the shell:

  1. single quoting (e.g. 'some text') – serves two purposes
    • it groups together all text inside the quotes into a single token
    • it tells the shell not to "look inside" the quotes to perform any evaluation
      • all metacharacters inside the single quotes are ignored
      • in particular, any environment variables in single-quoted text are not evaluated
  2. double quoting (e.g. "some text") – also serves two purposes
    • it groups together all text inside the quotes into a single token
    • it allows environment variable evaluation, but inhibits some metacharcters
      • e.g. asterisk ( * ) pathname globbing and some other metacharacters
    • double quoting also preserves any special characters present in the text
      • e.g. newlines (\n) or Tabs (\t)
  3. backtick quoting (e.g. `date`)
    • evaluates the expression inside the backtick marks ( ` )
    • the standard output of the expression replaces the text inside the backtick marks ( ` )
    • note that the syntax $(<expression>) is equivalent to `<expression>`

Note that the quote characters themselves ( '  "  ` ) are metacharacters that tell the shell to "start a quoting process" then "end a quoting process" when the matching quote is found. Since they are part of the processing, the enclosing quotes are not included in the output.

Always use single ( ' ) or double ( " ) quotes when you define an environment variable whose value contains spaces so that the shell sees the quoted text as one item.

Single vs double quotes examples:

echo "My Unix group is $MY_GROUP"   # The text "$MY_GROUP" is evaluated and its value substituted  
echo 'My Unix group is $MY_GROUP'   # The text "$MY_GROUP" is left as-is

foo="My USER name is $USER"; echo $foo         # The text "$USER" is evaluated and its value substituted
foo='My USER name is $USER'; echo $foo         # The text "$USER" is left as-is

FOO="Hello world!"
echo "The value of variable 'FOO' is \"$FOO\""  # Escape the double quotes inside double quotes

If you see the greater than ( > ) character after pressing Enter, it can mean that your quotes are not paired, and the shell is waiting for more input to contain the missing quote of the pair (either single or double). Just use Ctrl-c to get back to the command prompt.

Backtick evaluation quoting examples:

date          # Calling the date command just displays date/time information
echo date     # Here "date" is treated as a literal word, and written to output
echo `date`   # The date command is evaluated and its output replaces the command

today=$( date );          echo $today  # environment variable "today" is assigned today's date
today="Today is: `date`"; echo $today  # "today" is assigned a string including today's date

More at: Intro Unix: Writing text: Quoting in the shell

Redirection

So far text we've been working with output to standard output, which I keep reminding you is mapped to your Terminal. But you can redirect text elsewhere.

Recall the three standard Unix streams: they each have a number, a name and redirection syntax:

  • standard output is stream 1
    • redirect standard output to a file with a the > or 1> operator
      • a single > or 1> overwrites any existing data in the target file
      • a double >> or 1>> appends to any existing data in the target file
  • standard error is stream 2
    • redirect standard error to a file with a the 2> operator
      • a single 2> overwrites any existing data in the target file
      • a double 2>> appends to any existing data in the target file

If you want output to go to both the Terminal and a file, you can use the tee command (or tee -a to append).

Note that the > redirection metacharacter sends its output to a file, not to another program's standard input stream as with the | pipe metacharacter. (There are some cases where redirection involves something other than a file, but that's a topic for the Advanced Bash scripting class.)

More at: Intro Unix: Writing text: Redirection

Errors, output and their streams

Any time a bash command encounters an error, diagnostic error information is written to standard error, not to standard output!

When executing commands you will want to manipulate standard output and standard error appropriately – especially for 3rd party programs.

You can see that error and output streams are different by directing one or the other to the /dev/null "global trash can"

ls haiku.txt xxx.txt                # displays both output and error text on the Terminal
ls haiku.txt xxx.txt 2>/dev/null    # displays only output text on the Terminal
ls haiku.txt xxx.txt 1>/dev/null    # displays only error text on the Terminal

# And this syntax (2>&1) sends standard output to outerr.log and standard error to the
# same place as standard out. So data from both standard output and standard error
# will be written to outerr.log
ls haiku.txt xxx.txt 1>outerr.log 2>&1

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File systems, files, and file manipulation

Let's review Intro Unix: Files and File Systems. The most important takeaways are:

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