Merge pull request #63 from nesi/dini-dev

add setup.sh

setup.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# Color codes
+YELLOW='\033[1;33m'
+GREEN='\033[1;32m'
+NC='\033[0m' # No Color
+BOLD='\033[1m'
+
+# Ask for the working directory
+echo -e "${YELLOW}Provide the path to working directory for apsim_simulations:${NC} \c"
+read -r working_dir
+
+# Check if the directory exists, if not create it
+if [ ! -d "$working_dir" ]; then
+    mkdir -p "$working_dir"
+    echo "Created directory: $working_dir"
+fi
+
+# Copy the R script
+cp 03-generate-config-files/generate_apsim_configs.R "$working_dir"
+
+# Copy the Snakefile_txt
+cp 08-snakemake/Snakefile_txt "$working_dir"
+
+# Copy the Snakefile_apsimx
+cp 08-snakemake/Snakefile_apsimx "$working_dir"
+
+# Print completion message
+echo -e "\nSetup is complete. Switching to working directory now."
+
+# Change to the working directory
+cd "$working_dir" || exit
+
+# Print current directory to confirm
+echo -e "${GREEN}${BOLD}Current working directory: $(pwd)${NC}"