.PHONY: help build run test clean

# Default target
help:
	@echo "PocketMiner - Cryptic Pocket Prediction Tool"
	@echo ""
	@echo "Available targets:"
	@echo "  make build       - Build Docker image (conda-based, includes all dependencies)"
	@echo "  make run         - Run test prediction (requires test.pdb)"
	@echo "  make test        - Run Nextflow pipeline on test data"
	@echo "  make clean       - Clean up generated files"
	@echo "  make shell       - Open shell in Docker container"
	@echo "  make download-example - Download example PDB file"
	@echo ""

# Build Docker image (conda-based with all dependencies)
build:
	@echo "Building PocketMiner Docker image (conda-based)..."
	docker build -t pocketminer:latest .
	@echo "Build complete!"

# Run single test prediction
run:
	@if [ ! -f test.pdb ]; then \
		echo "Error: test.pdb not found. Please provide a test PDB file."; \
		exit 1; \
	fi
	@echo "Running PocketMiner prediction on test.pdb..."
	docker run --rm \
		-v $(PWD):/data \
		pocketminer:latest \
		python /workspace/entrypoint.py \
			--pdb /data/test.pdb \
			--output-folder /data/output \
			--output-name test
	@echo "Results saved to output/"

# Run Nextflow pipeline
test:
	@echo "Running Nextflow pipeline..."
	nextflow run main.nf
	@echo "Pipeline complete!"

# Clean generated files
clean:
	@echo "Cleaning up..."
	rm -rf output/
	rm -rf .nextflow/
	rm -f .nextflow.log*
	rm -rf work/
	rm -rf results/
	rm -f *.npy *.txt
	@echo "Clean complete!"

# Open shell in container
shell:
	docker run --rm -it \
		-v $(PWD):/data \
		pocketminer:latest \
		/bin/bash

# Download example PDB (if internet available)
download-example:
	@echo "Downloading example PDB (1HSG - HIV protease)..."
	wget -O test.pdb https://files.rcsb.org/download/1HSG.pdb
	@echo "Example downloaded as test.pdb"