Writing Shell Scripts
Creating a Script
Shell scripts are convenient ways of running multiple commands. These scripts usually end with .sh. Let's use nano to create a shell script that says the date. First move to our scripts_folder:
cd ../scripts_folder/
Now create a script called "first_script.sh" with the following contents:
first_script.sh
#!/bin/bash
# run the date command
date
You'll note we use #!/bin/bash to make sure this is a bash shell script. When we start using other programming languages (like python) this will be swapped out with #!/bin/ptyhon. We also have a line that starts with a #. This is called a comment. Comments aren't read as code, they are just plain text we can add to give our commands/code context. Comments are very useful in making your code readable. We should also note that we can't run our script just yet. To run our script we will need to change the permissions on it with the chmod command:
chmod +x first_script.sh
This command allows us to execute our script. To execute our script we can enter the following:
./first_script.sh
first_script.sh
Sat May 13 13:00:45 EDT 2023
Variables
Now let's make our script more complicated with a variable (basically a word that represents some value):
first_script.sh
#!/bin/bash
# define a variable
initial="Today is:"
# echo the variable and date
echo $initial
date
Here we see that we have text ("Today is:") that is assigned to initial, which we reference with a $ sign. To run this script we will enter the following:
./first_script.sh
first_script.sh
Today is:
Sat May 13 13:00:45 EDT 2023
Functions
We can create a function using shell scripting with the following syntax:
function_name (){
command
}
To call that function we write out function_name(). Let's modify our script to add a function!
first_script.sh
#!/bin/bash
# define a variable
initial="Today is:"
# echo the variable and date
echo $initial
date
# define a function to print the first column of the first argument you give the script
first_col() {
awk '{print $1}' $1
}
# call this function
first_col $1
In our function, we ask it to print the first column of the first argument passed to the function. When we call the function, we ask it to apply this function to the first argument we give the script itself. So let's run this script with the meta.txt file as our argument:
./first_script.sh
output
Today is:
Sat May 13 13:30:30 EDT 2023
Run
SRR1219879
SRR1219880
Loops
We can use loops to perform repetitive tasks. Loops follow the following syntax:
for variable in list
do
command $variable
done
Let's modify our script to use a loop to examine the first line of all files in working directory:
first_script.sh
#!/bin/bash
# define a variable
initial="Today is:"
# echo the variable and date
echo $initial
date
# define a function to print the first column of the first argument you give the script
first_col() {
awk '{print $1}' $1
}
# call this function
first_col $1
# make a loop to examine the first line of all files in working directory
for file in *
do
head -n 1 $file
done
To run the script we will enter the following:
./first_script.sh
output
Today is:
Sat May 13 13:30:30 EDT 2023
Run
SRR1219879
SRR1219880
#!/bin/bash