I have a bash script where I use singularity exec to run a program from inside the container. I want to call this script in R using the system() function. Everything works fine until it reaches the line containing singularity exec, where I get the error : "./script.sh: line 22: singularity: command not found "
The bash script works well when I call it directly in command line.
How could I make it work?
Thank you.