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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.

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  • Isn't it that the error message is not command not found, but something like bash: singularity: command not found? Commented Mar 12, 2024 at 13:19
  • @user1934428 It's "./script.sh: line 22: singularity: command not found" Commented Mar 12, 2024 at 13:21
  • 1
    Then you obviously have to fix your PATH.... Commented Mar 12, 2024 at 13:48
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