04-shell-script.md

Shell Rscript

Learning Objectives:

• Invoking and running R scripts as shell scripts
• Review of shell scripts
• Execute some scripts

---

Shell Scripts

A shell script is simply a text file that contains a series of shell commands that you want to run in sequence.

I’ll show you an example of a simple shell script, and then I will describe how to write a shell script for R.

For this example I’m assuming that you are working with the bash shell.

This example is based on the file today.sh, which is available in the scripts/ folder of this tutorial. If you look at the contents of today.sh you should see the following lines:

#!/bin/bash

echo "The current time and day is"
date

Basically, today.sh is a script that prints a message and the current’s date information.

When creating a shell script file, you must specify the shell you are using in the first line of the file. In this case we have: #!/bin/bash. Typically the pound sign # is used as a comment line. However, the first line of a shell script file is a special case. The set of characters #! is often referred to as the shebang. The shebang tells the shell what shell to run the script under (bash in this example).

If you try to run the file by simply typing its name on the command line, you will be disappointed:

today.sh
-bash: today.sh: command not found

Even though today.sh is declared as a file that the bash should execute, the error message indicates that bash is not able to find the command.

This issue has to do with the way the bash shell finds commands. bash uses an environment variable called PATH to find commands. The PATH variable is set to look for commands only in a handful of directories. To get the shell to find the today.sh script, you have two options:

• Add the directory where your shell script file is located to the PATH.

• Use an absolute or relative file path to reference your shell script.

We’ll choose the second option, by referencing the file in the scripts/ directory using the dot operator:

./today.sh
-bash: ./today.sh: Permission denied

Even though the shell did find the script, there’s still a problem: we don’t have permission to execute the file. This can be solved quickly by changing the permissions with the chmod command:

chmod u+x today.sh

Now you should be able to run today.sh without problems:

./today.sh

---

R shell scripts

Now that we’ve seen how to write a shell script file, we can discuss how to do something similar with an R script.

Running R from a shell script involves writing a shell script including R functions and then calls to these functions. For instance, consider the file hello in the scripts/ directory:

#!/usr/bin/env Rscript
hello_world <- function(){
   cat('hi! I'm an R script\n')
}

hello_world()

This script calls the function hello_world() which prints a dummy message. The important thing is the first line of the file containing the shebang and telling the shell where to find the program (i.e. Rscript) to run the script: #!/usr/bin/env Rscript.

The next step is to change the permissions of the file to make it executable:

chmod u+x hello

Assuming that hello is in your current directory, you can run it like so:

./hello

Example: Area of Rectangle

The file area.txt in the scripts/ folder is another shell script that calculates the area of rectangle of length 3 and width 5:

#!/usr/bin/env Rscript

len <- 3
width <- 5
area <- len * width

cat("Area of a rectangle:\n")
cat("length = ", len, "\n")
cat("width  = ", width, "\n")
cat("area   = ", area, "\n")

After changing the permission of the file:

chmod u+x area.txt

you can execute it like this:

./area.txt

Area of a rectangle:
length =  3 
width  =  5 
area   =  15 

---

Passing arguments

If you want to pass arguments to your script, remember to use the function commandArgs(trailingOnly = TRUE). Here’s the same example presented in the third section 03-script, although in this case the script file is called normal-vector.txt:

#!/usr/bin/env Rscript

# Generates a random vector following a normal distribution.
# Values for 'n', 'mean', 'sd' are expected (in that order).

# reading arguments ('n', 'mean', 'sd')
args <- commandArgs(trailingOnly = TRUE)

n <- as.numeric(args[1])
mean <- as.numeric(args[2])
sd <- as.numeric(args[3])

x <- rnorm(n, mean, sd)
cat(x, '\n')

Assuming that you change the file permissions, you can run it as:

./normal-vector.txt 10 5 1

4.622793 3.62027 4.268408 5.323577 6.735752 6.647538 7.315079 5.048416 5.460435 7.244645 

---

Bash R script

Here’s one more example, slightly different. In this case we have a bash script that instead of using the command Script, it uses the R command. The file is bash-example.sh

#!/bin/bash

# creates a csv file with log-transformed
# variable 'mpg' and 'hp' from data set 'mtcars'

R --slave <<EOF
log_mtcars <- function()
{
    log_mpg <- log(mtcars$mpg)
    log_hp <- log(mtcars$hp)
    logdata <- data.frame(log_mpg, log_hp)
    write.csv(logdata, "log-mtcars.csv")
}

log_mtcars()

EOF

Now, make this file executable by

chmod +x bash-example.sh

To run the R function included in this file type

./bash-example.sh

---