bash Configuration

We do a lot of work (especially when working remotely) using the Linux command-line interface in terminal sessions. All of our documentation assumes that the particular “flavour” of that interface you are using is bash. For historical reasons, Linux and Unix command-line interfaces are called “shells”. So, when someone talks about using bash, or “the shell”, they mean typing commands into a terminal session.

You can find out what shell you are using in most terminal sessions with the command:

echo $shell

If the shell you are using is bash, the output of that command will most likely be:

/bin/bash

In order to make bash work well for us on the Waterhole workstations and other MOAD computers, we have to create two configuration files in our home directory:

1. .bash_profile

2. .bashrc

If you are new to bash or the Linux command-line, ask Doug for a link to the PDF of “The Linux Command Line” book by William E. Shotts, Jr. For quick reminders about some of the most often used Linux commands this Unix Shell Quick Reference page from Software Carpentry is also helpful.

Create .bash_profile

New MOAD accounts on the Waterhole workstations are created completely empty. So, the first thing we need to do is create a file called .bash_profile in the home directory. Your home directory is the one that you land in when you ssh to a remote computer, or when you start up a terminal session.

Note

You only need to do this once on the MOAD machines because you home directory is shared across all of the machines.

You probably don’t need to do this on your laptop because .bash_profile likely already exists, and you shouldn’t change it until you know what you are doing and why.

Use the nano text editor to create a new .bash_profile file:

$ nano .bash_profile

The . at the beginning of the file name is important! Type, or copy/paste the following lines into the file:

if [ -f "$HOME/.bashrc" ]; then
    . "$HOME/.bashrc"
fi

# set PATH so it includes user's private bin dirs if they exists
if [ -d "$HOME/.local/bin" ] ; then
    PATH=$HOME/.local/bin:$PATH
fi
if [ -d "$HOME/bin" ] ; then
    PATH=$HOME/bin:$PATH
fi

Then save the file, and exit nano.

When bash starts up in a new terminal session it looks for the .bash_profile file and executes the commands in it. Those commands above tell bash to check to see if another file called .bashrc exists and, if so, execute the commands in it. They also tell bash about some user-specific directories that it should look in to find commands.

It will come as no surprise that the next thing we are going to do is Create .bashrc.

Create .bashrc

Note

You only need to do this once on the MOAD machines because you home directory is shared across all of the machines.

You probably don’t need to do this on your laptop because .bashrc likely already exists. But if you like some of the aliases below you might want to add them to .bashrc on your laptop.

Use the nano text editor to create a new .bashrc file:

$ nano .bashrc

The . at the beginning of the file name is important! Type, or copy/paste the following lines into the file:

## Environment variables
# Shorter shell prompt
PS1="\h:\W$ "

# Pager setup
export PAGER=less
export LESS=-R

# Make nano the default full-screen editor
export EDITOR=nano
export VISUAL=nano

## Aliases
alias df="df -h"
alias du="du -h"
alias grep="grep --color=auto"
alias ls="ls --color=auto -F"
alias la="ls -a"
alias ll="ls -al"
alias rm="rm -i"

Warning

alias ls="ls --color=auto -F" does not work on MacOS. It produces an error. Instead, to get coloured output from ls you have to set the CLICOLOR environment variable to True by putting:

export CLICOLOR=True

in your .bashrc file.

When you are done, save the file, and exit nano.

You will have to leave the shell by typing the command:

$ exit

and then ssh into the workstation again in order for bash to use your new .bash_profile and .bashrc files.

.bashrc Command Explanations

This section briefly explains what each of the command in the section above mean.

PS1="\h:\W$ "

shortens your command-line prompt so that it shows just the name of the machine that you are on and the directory that you are currently in instead of the whole path to that directory.

export PAGER=less

forces programs and commands that want to display output page by page to use less as their pager.

export LESS=-R

forces less to allow control sequences that change the colour of its output

If you are not a fan of the vi editor you can set the EDITOR and VISUAL environment variables to the command for your favourite editor and export them. For emacs use:

export EDITOR=nano
export VISUAL=nano

tells the system to use nano as your default editor. If you prefer a different editor, substitute its name. Other common choices are emacs, vim, or vi.

alias df="df -h"

modifies the df command that shows how much disk space is free to use human-friendly units like G for gigabytes instead of its default of 1K blocks.

alias du="du -h"

similarly modifies the du command that shows disk space usage.

alias grep="grep --color=auto"

modifies the grep command for finding strings in files to show its output in colour.

alias ls="ls --color=auto -F"

modifies the ls command for listing directory contents to show its output in colour. It also make ls show extra characters after the file/directory names to indicate special properties; e.g. append / to directory names, * to executable files, @ to symbolic links, etc.

alias la="ls -a"

creates a new command, la, that is an alias for ls -a to make ls show hidden files and directories (whose names start with the . character). Aliases are cumulative, so, la will also be in colour and have appended indicator characters because of the way ls is aliased in the line above.

alias ll="ls -al"

creates a new command, ll, that is an alias for ls -al to make ls show lots of details (permissions, owner and group, file size, and last modification date/time) about files (often called a long listing) and include hidden files/directories in the listing.

alias rm="rm -i"

modifies the rm command for removing files to always prompt you to confirm that you really want to delete the file(s).

Note

You can find more information about any of the commands in the aliases above by using the man command; e.g. to find out more about the options available to control file and directory listings that the ls produces, use man ls, or Google something like “linux ls” or “man ls”.