Run ED singularity container

Uses base::system2 to run ED or EDR via a Singularity container.

run_ed_singularity(img_path, ed2in_path, app = "ED",
  singularity_args = NULL, ...)

Arguments

img_path	Path to Singularity container (usually a .simg file)
ed2in_path	Path to ED2IN file.
app	Singularity "app" to run. Either "ED" or "EDR".
singularity_args	Additional arguments to be passed to singularity run (before)
Additional	arguments to base::system2

Details

On some systems, to run Singularity properly, you will need to bind additional paths. To do this, pass the arguments as a character vector to singularity_args. For instance:

bindpaths <- c("/scratch", "/data")
run_ed_singularity(..., singularity_args = paste("--bind", bindpaths))

By default, base::system2 prints the output to the console. To store standard ED output in a variable as a character vector, set stdout = TRUE. To redirect all output to the variable, including GCC exceptions, use stderr = TRUE (this will automatically set stdout = TRUE as well). Output can also be redirected to a file via stderr = "/path/to/file.log".