Linux/Bash Command Line Primer


  • Understand how what the command line is
  • Understand basic command line syntax
  • Know the functions of the most common commands

Command Line Intro

The Command Line (sometimes called ‘the terminal’, ‘shell’, ‘Bash’, etc.) is an alternative to using a graphical interface (GUI, pronounced “gooey”) or point-and-click interfaces to operate a computer. Actually, command line came before GUIs and although it’s older, it is the most popular way for researchers to use the computer and installed software. Imagine trying to explain to someone how to make a recipe using only pictures (not even video). You would need a lot of photos! If they wanted to modify the recipe for someone else, they would need to take new photos. While photos help a cook, having written instructions is much clearer. Using the command line, we can explicitly write every single instruction we want the computer to run; this means our analysis is always completely documented.


It does take time to learn the command line, and some things about the command line are difficult the first time you try. This primer will cover just the basics needed to make the tutorial easier to understand. To learn more, we suggest the Software Carpentry lessons on the UNIX command line.

Command Line Syntax

As the name suggests, everything run at the command line is a command. The Syntax for a command looks like this:

command [options]

The [options] are some options that modify the command, and as the name implies these are optional. Some commands may take an <input>; here the pointed brackets suggest that the input is required.

One common command is the ls (list) command. Typing this will show the contents of the current directory:


To see what directory you are in, you can use the pwd command to see the current working directory:


The ls command takes options. You can list the content of a specific directory. For example to see the contents of /home/gea_user/ you would try:

ls /home/gea_user/

Note there is always a space between a command (ls) and its inputs or options (/home/gea_user/)

Command Glossary

These are some commands you are likely to see:

  • cat - Concatenate: Print a file to the screen
    • Example: cat file.text
  • cd - Change Directory: Change the working directory to a new directory
    • Example: cd /path/to/desired/new/directory
  • cut - Cut: Choose a column from a tab-delimited file (spreadsheet)
    • Example: cut -f (column number to choose) file.txt
  • head - Head: See the first few lines of a file
    • Example: head -n (number of lines to show) file.txt
  • ls - List: Show the content of a directory
    • Example: ls /directory/to/show
  • mkdir - Make directory: Make a new directory/folder
    • Example: mkdir name_of_new_directory
  • mv - Move: Move a file(s) or directory
    • Example: mv /file/at/old/location/ /new/location/to/move/to
  • rm - Remove: Delete a file/directory (must use -r option to delete a directory)
    • Example: rm name_of_file_to_delete
  • wget - W get: Download a file from a URL
    • Example: wget

More Command Line Syntax Tips

Pay attention to spaces and special characters

The Command Line requires you to be very exact in your syntax. In general, you don’t want to have file names with special characters (e.g. !#$%^&* etc.). Also, you cannot use spaces in file names (use underscore or dash instead).


In some cases you will see the wildcard character ‘*’. This asterisk generally means match any character. For example the command

mv *.html /directory

Would mean “move any file as long as it ends in “.html” to a place called /directory

Long Commands and Loops

Long Commands

Sometimes you will see a command that looks like this:

for file in *_trimmed.fastq.gz; do output=$(basename --suffix=.fastq.gz_trimmed.fastq.gz $file)_quant; kallisto quant\

The backslash (\) is just a way of splitting up the command over multiple lines to make it easier to read. We could also write the same command like this (more difficult to read):

for file in *_trimmed.fastq.gz; do output=$(basename --suffix=.fastq.gz_trimmed.fastq.gz $file)_quant;
kallisto quant --single --threads=8 --index=/home/gea_user/rna-seq-project/transcriptome/Mus_musculus.GRCm38_index
--bootstrap-samples=25 --fragment-length=200 --sd=20 --output-dir=$output;


You will also see loops with a syntax that begins with a statement like ‘for’ or ‘while’. For example:

for trimmed_file in /home/gea_user/rna-seq-project/trimmed-reads/*_trimmed.fastq.gz
 fastqc $trimmed_file


while read line; do prefetch $line; done<finalsamples.txt; done

A loop usually takes several files and performs one or more operations to that file. See the Software Carpentry loop lesson for more on this.


At the shell you will sometimes see a ‘$’ in front of a word. This ‘$’ indicates that the word is a variable. You will usually see this inside of loops and the Software Carpentry loop lesson also goes into further explanation.


The website Explain Shell allows you to take a line of Linux code and break it down into an annotated explanation.