Bash scripts

Anything you can do on the shell can be placed in a bash (shell) script.

Variables

We can save variables under almost any name.

Variables can be string type:

evomics="Workhop_on_genomics_2024"

data="genome_assembly_file.fasta"

path="/home/genomics/workshop_materials/unix"

Integer type:

num=5

or float type:

pi=3.14

We can refer to the variables using a dollar sign:

$evomics

${evomics}

Bash loops

for loops

Loop over files inside a directory:

for file in ./unix/working_directory/*fastq

do

commands $file

done

Loop over files that we stored inside a variable:

files="file1

file2

file3

file4"

for file in $files

do

commands $file

done

while loops

while read line

do

command $line

done

We can pipe the command ls -l to this script to run the command on each of the files listed.

Stay informed while your script runs!

If we want to print messages to the standard output while the script is running we can do that using the echo command. This is specially useful when running a long pipeline of multiple commands, so that we can keep track of the stage that is currently running.

for file in ./unix/working_directory/*fastq

do

echo "Command 1 is running on $file"

command1 $file

echo "Command 2 is running on $file"

command2 $file

done

Some tricks for keeping order and good names on files

Sometimes when we run a for loop on multiple files, we want to avoid carrying all the file format tags in each output file. 

for file in ./unix/working_directory/*fastq

do

file_name=$(basename $file ".fastq")

command1 $file -out ${file_name}_command1.fastq

done

It is the same as:

for file in ./unix/working_directory/*fastq

do

file_name=$(basename $file ".fastq")

command1 $file -out "$file_name"_command1.fastq

done

When using the variable $file_name, we need to separate what is the variable and what is the string of the output name we want to give.
Just by writing: $file_name_command1.fastq, we would be trying to call for a variable name that does not exist.

A good method is to always put variables in our code within curly brackets after the dollar sign: ${file_name}

Alternativelly, we have to remember to add the quotation around the variable when we need to use it in combination with other text.