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,
...
)
Path to Singularity container (usually a .simg
file)
Path to ED2IN file.
Singularity "app" to run. Either "ED" or "EDR".
Additional arguments to be passed to singularity run
(before)
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"
.