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Run ED singularity container

Source: R/run_ed_singularity.R
run_ed_singularity.Rd

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

Usage

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".