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Use flepimop-inference-slot cmd directly
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Per an @pearsonca suggestion.
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TimothyWillard committed Dec 3, 2024
1 parent d883bfb commit 7f9d3f0
Showing 1 changed file with 7 additions and 1 deletion.
Original file line number Diff line number Diff line change
Expand Up @@ -128,8 +128,14 @@ foreach(seir_modifiers_scenario = seir_modifiers_scenarios) %:%
log_file <- paste0(
"log_inference_slot_", config$name, "_", opt$run_id, "_", flepi_slot, ".txt"
)
inference_slot_cmd <- unname(Sys.which("flepimop-inference-slot"))
if (inference_slot_cmd == "") {
stop(
"`flepimop-inference-slot` not found in PATH, unable to run inference slot"
)
}
command <- c(
file.path(opt$flepi_path, "flepimop", "main_scripts","inference_slot.R"),
inference_slot_cmd,
"-c", opt$config,
"-u", opt$run_id,
"-s", opt$seir_modifiers_scenarios,
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