run_ed_singularity.Rd
Uses base::system2 to run ED or EDR via a Singularity container.
run_ed_singularity(img_path, ed2in_path, app = "ED", singularity_args = NULL, ...)
img_path | Path to Singularity container (usually a |
---|---|
ed2in_path | Path to ED2IN file. |
app | Singularity "app" to run. Either "ED" or "EDR". |
singularity_args | Additional arguments to be passed to |
Additional | arguments to base::system2 |
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"
.