Basic scripting in R script

Code

Our executable written in R, echo-next.R:

args <- commandArgs(trailingOnly = TRUE)
filename <- args[1]
cat(filename,"\n")

The output of commandArgs is a vector -- if you have multiple arguments, you can reference each item using R's usual notation (args[1], args[2], etc.). See R documentation on commandArgs for details.

We can use the script on the command line, assuming R is installed and on the PATH:

[user@login]$ Rscript echo-next.R data.csv
data.csv

Wrapper script

We can now write a wrapper script! This script checks that one argument is passed, and also allows room for pre- and post-processing in this simple workflow.

Our wrapper script written in bash, wrapper.sh:

#!/bin/bash

# Check if an argument is provided
if [ $# -ne 1 ]; then
    echo 'Please use one argument. Usage: wrapper.sh [arg]'
    exit 1
fi

# Set filename variable to the first argument to the bash script
filename=$1

echo 'Pre-processing could go here.'

# Run code
Rscript echo-next.R ${filename}

echo 'Post-processing could go here.'

Ensure wrapper.sh is executable with chmod +x wrapper.sh before running it on the command line:

[user@login]$ chmod +x wrapper.sh
[user@login]$ ./wrapper.sh
Please use one argument. Usage: wrapper.sh [arg]
[user@login]$ ./wrapper.sh data.csv
Pre-processing could go here.
data.csv
Post-processing could go here.

Passing arguments with the HTCondor submit file

Now that we've understood how arguments work in R and how to write simple wrapper scripts that pass those arguments, we can pass arguments in HTCondor's submit file by specifying the arguments attribute, as shown in this excerpt:

# Create custom variable called "data"
data = data.csv

# Specify the executable & arguments
executable = wrapper.sh
arguments = $(data)