#!/bin/bash

# Set up directory structure for BioEmu workflow
BASE_DIR="/mnt/OmicNAS/private/old/olamide/bioemu"

# Create necessary directories
mkdir -p ${BASE_DIR}/input
mkdir -p ${BASE_DIR}/output
mkdir -p ${BASE_DIR}/cache
mkdir -p ${BASE_DIR}/scripts

# Copy FASTA files
cp villin_headpiece.fasta ${BASE_DIR}/input/
cp trp_cage.fasta ${BASE_DIR}/input/

# Copy scripts
cp calculate_gibbs.py ${BASE_DIR}/scripts/
chmod +x ${BASE_DIR}/scripts/calculate_gibbs.py

echo "Directory structure set up at ${BASE_DIR}"
echo "FASTA files and scripts copied"