add docker_climatearray2rds.sh

docker_climatearray2rds.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+source run_container.sh
+
+# Check for required arguments
+if [ $# -lt 2 ]; then
+    echo "Usage: $0 <input_directory> <output_directory> <extra-args>"
+    exit 1
+fi
+
+# Convert relative paths to absolute paths
+INPUT_DIR=$(realpath "$1")
+OUT_DIR=$(realpath "$2")
+
+shift 2
+
+# Run the container with mounted directories
+run_with_mounts "$INPUT_DIR" "$OUT_DIR" \
+climatearray2rds -i /home/biodiversity-horizons/data-raw \
+-o /home/biodiversity-horizons/outputs "$@"

scripts/main.R

@@ -196,22 +196,6 @@ run_climatearray2rds <- function(args) {
   print("File converted successfully!")
 }
 
-safe_parse_opts <- function(opt_parser, args) {
-  # Function to safely parse the options. Shows the help if there's an error.
-  opt <- tryCatch(
-    {
-      opt <- parse_args(opt_parser, args = args)
-      opt
-    },
-    error = function(e) {
-      cat("Error parsing arguments:", e$message, "\n")
-      opt <- parse_args(opt_parser, args = c("--help"))
-      FALSE
-    }
-  )
-  return(opt)
-}
-
 run_exposure <- function(args) {
   source("scripts/exposure_workflow.R")
   option_list <- list(