12  Appendix: Configuring your Shell

12.1 .bashrc: Where do I put my configuration?

There is a file in your home directory called .bashrc. This is where you can customize the way the Bash shell behaves.

There are 2 things you should know how to set:

  • Aliases
  • Environment Variables, especially $PATH

12.2 Aliases

Aliases are shortcuts for commands. You can specify them using alias as a line in your .bashrc file:

alias ll='ls -la'

We are defining an alias called ll that runs ls -la (long listing for directory for all files) here. Once

Some people even add aliases for things they mistype frequently.

12.3 Environment Variables

Environment variables are variables which can be seen globally in the Linux (or Windows) system across executables.

You can get a list of all set environment variables by using the env command. Here’s an example from my own home system:

env
SHELL=/bin/bash
NVM_INC=/home/tladera2/.nvm/versions/node/v21.7.1/include/node
NAME=2QM6TV3
PWD=/home/tladera2
LOGNAME=tladera2
[....]

One common environment variable you may have seen is $JAVA_HOME, which is used to find the Java Software Development Kit (SDK). (I usually encounter it when a software application yells at me when I haven’t set it.)

You can see whether an environment variable is set using echo, such as

echo $PATH
/home/tladera2/.local/bin:/home/tladera2/gems/bin:/home/tladera2/.nvm/versions/node/v21.7.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/ [....]

12.3.1 Setting Environment Variables

In Bash, we use the export command to declare an environment variable. For example, if we wanted to declare the environment variable $SAMTOOLS_PATH we’d do the following:

# works: note no spaces
export SAMTOOLS_PATH="/home/tladera2/miniconda/bin/"

One thing to note is that spacing matters when you declare environment variables. For example, this won’t declare the $SAMTOOLS_PATH variable:

# won't work because of spaces
export SAMTOOLS_PATH = "/home/tladera2/miniconda/bin/"

Another thing to note is that we declare environment variables differently than we use them. If we wanted to use SAMTOOLS_PATH in a script, we use a dollar sign ($) in front of it:

${SAMTOOLS_PATH}/samtools view -c $input_file

In this case, the value of $SAMTOOLS_PATH will be expanded (substituted) to give the overall path:

/home/tladera2/miniconda/bin/samtools view -c $input_file

12.3.2 A Very Special Environment Variable: $PATH

The most important environment variable is the $PATH variable. This variable is important because it determines where to search for software executables (also called binaries). If you have softwware installed by a package manager (such as miniconda), you may need to add the location of your executables to your $PATH.

We can add more directories to the $PATH by appending to it. You might have seen the following bit of code in your .bashrc:

export PATH=$PATH:/home/tladera2/samtools/

In this line, we are adding the path /home/tladera2/samtools/ to our $PATH environment variable. Note that how we refer to the PATH variable is different depending on which side the variable is on of the equals sign.

NoteOrder matters in your $PATH

The order of directories is the order in which bash will look for executables. If you install software yourself on gizmo (using make or such), you should prepend the binary directory with your software to the $PATH:

export PATH=/home/tladeras/samtools/:$PATH

TLDR: We declare the variable using export PATH (no dollar sign) and we append or prepend to this variable using $PATH (with dollar sign). This is something that trips me up all the time.

NoteFor FH Users

In general, when you use environment modules on gizmo, you do not need to modify your $PATH variable. You mostly need to modify it when you are compiling executables so that the system can find them. Be sure to use which to see where the environment module is actually located:

which samtools

12.3.3 Making your own environment variables

One of the difficulties with working on a cluster is that your scripts may be in one filesystem (/home/), and your data might be in another filesystem (/fh/fast/). And it might be recommended that you transfer over files to a faster-access filesystem (/fh/temp/) to process them.

You can set your own environment variables for use in your own scripts. For example, we might define a $TCR_FILE_HOME variable:

export TCR_FILE_HOME=/fh/fast/my_tcr_project/

to save us some typing across our scripts. We can use this new environment variable like any other existing environment variable:

#!/bin/Bash
export my_file_location=$TCR_FILE_HOME/fasta_files/
Note.bashrc versus .bash_profile

Ok, what’s the difference between .bashrc and .bash_profile?

The main difference is when these two files are sourced. bash_profile is used when you do an interactive login, and .bashrc is used for non-interactive shells.

.bashrc should contain the environment variables that you use all the time, such as $PATH and $JAVA_HOME for example.

You can get the best of both worlds by including the following line in your .bash_profile:

source ~/.bashrc

That way, everything in the .bashrc file is loaded when you log in interactively.