Intro to Bash

bashrc

A good place to start is your .bashrc file, which acts as a set of ‘start up’ instructions whenever you open your terminal. The .bashrc file is located in ~/.bashrc i.e your home directory. You may never have noticed it because it is a hidden file (any file with a dot prefix is hidden). To show hidden files when running ls, use ls -a.

Commonly included items in a .bashrc file are:

Aliases: custom short hand commands that are aliases for longer, tricky to remember commands.
Terminal colors: not overly important..
$PATH variables: a list of directories that are searched for executables.

Aliases

Below are a set of aliases I use frequently which may save you some time. Copy the contents of the code block below to your ~/.bashrc file and save the file. To initiate the changes, open a new terminal or run source ~/.bashrc.

# bash alias
alias l="ls -lhg --color=auto"
alias ls='ls --color=auto'
alias tarzip="tar -cvzf"
alias tarunzip="tar -xvzf"
alias vbrc="vi ~/.bashrc"
alias sbrc="source ~/.bashrc"
alias lugh="ssh bdigby@lugh.nuigalway.ie"

Inputrc

A very handy trick is the ability to scroll through your history based on a partial string match to a command previously run. You will need to create the file: ~/.inputrc:

~/.inputrc :

#Page up/page down
"\e[B": history-search-forward
"\e[A": history-search-backward

$include /etc/inputrc

Now add the following line to your ~/.bashrc file:

#auto complete
export INPUTRC=$HOME/.inputrc

Source both files to initiate the changes:

source ~/.bashrc
bind -f ~/.inputrc

Test it out by cycling through your history with the arrow keys, and (for example) typing cd and then press the arrow keys to cycle thorugh all previous cd commands (as opposed to the most recent command).

$PATH

I will demonstrate the utility of the $PATH variable I showed you in the tutorial.

Start by making a new directory and navigate to that directory:

mkdir -p ~/foo/bar/qux
cd ~/foo/bar/qux

Create a file, we are going to pretend this is an executable like fastqc or bowtie2 - the principle is the exact same.

touch executable && chmod 777 executable

In the ~/foo/bar/qux directory, we are able to “run” executable by typing ./executable. You can type ./exec and hit TAB to autocomplete the command.

Navigate to your $HOME directory and “run” the executable by file. We need to provide either the relative or absolute path to the executable:

# relative path
foo/bar/qux/executable

# absolute path
/home/barry/foo/bar/qux/executable

Add the /home/barry/foo/bar/qux/ directory to the $PATH variable:

export PATH=$PATH:/home/barry/foo/bar/qux/

Now type execu and hit TAB to autocomplete the command. You should be able to access executable from anywhere on your system. To confirm this, type which executable to view where the executable is located.

To make this permanent, add export PATH=$PATH:/home/barry/foo/bar/qux/ to your ~/.bashrc file.

Note

This will allow your system to see all files in foo/bar/qux/ and all subdirectories. For the sake of the demonstration I have only used one file.

Variable Expansion

When running a bioinformatics workflow, from a scripting perspective all we are doing is making sure that samples retain their correct names as they are passed to different file types (e.g fastq to bam).

You will need to have a concept of basename and variable expansion such that you can name samples correctly in an automated manner when scripting.

Note

please use the fastq files from Assignment one here

#!/usr/bin/env bash

    # place path to fastq files here (substitute your own)
    fastq_dir="/data/MA5112/week1/fastq"

    # we are reading R1 and R2 at once here (*{1,2}).
    for file in ${fastq_dir}/*{1,2}.fastq.gz; do

        # get the sample name (remove extension)
        # we will need this for naming outputs
        sample_name=$( basename $file .fastq.gz )

        # print sample name
        echo "File name without extension: $sample_name"

        # we still have _1 and _2 in the name for read 1 and 2 which messes up naming.
        # remove them before continuing
        base_name=$(basename $sample_name | cut -d'_' -f1,2)

        #print base name with R1 R2 (1 , 2) stripped:
        echo "File name without Read identifier: $base_name"

        # What if the process needs both R1 and R2? (e.g alignment)
        R1=${base_name}_1.fastq.gz
        R2=${base_name}_2.fastq.gz

        # sanity check below to see if R1 and R2 VAR are set properly:
        echo "Staging sample: $base_name"
        echo "Beginning to count lines in files..."
        lines_R1=$(zcat $fastq_dir/$R1 | wc -l)
        lines_R2=$(zcat $fastq_dir/$R2 | wc -l)
        echo "Done!"
        echo "$lines_R1 lines in $R1 and $lines_R2 lines in $R2"

        printf "\n\n"

        # make script pause for a sec to see output
        sleep 5

    done

Take your time going through this script. Personally, I would ‘comment out’ each line inside the for loop (add a # at the beginning of the line) and then run the script, removing comments as you gain understanding.

To run the script, type bash <scriptname>.sh in your terminal.