Olamide Isreal
42d4e6cb87
- Add Nextflow pipeline (main.nf) with Harbor container image - Add nextflow.config with k8s/k8s_gpu/standard profiles - Add params.json for TRS/WES parameter discovery - Add Dockerfile, entrypoint.py, meta.yml from original implementation - Update paths to use /omic/eureka/Pocketminer/ convention - Update .gitignore to allow params.json
67 lines
1.8 KiB
Makefile
67 lines
1.8 KiB
Makefile
.PHONY: help build run test clean
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# Default target
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help:
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@echo "PocketMiner - Cryptic Pocket Prediction Tool"
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@echo ""
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@echo "Available targets:"
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@echo " make build - Build Docker image (conda-based, includes all dependencies)"
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@echo " make run - Run test prediction (requires test.pdb)"
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@echo " make test - Run Nextflow pipeline on test data"
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@echo " make clean - Clean up generated files"
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@echo " make shell - Open shell in Docker container"
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@echo " make download-example - Download example PDB file"
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@echo ""
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# Build Docker image (conda-based with all dependencies)
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build:
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@echo "Building PocketMiner Docker image (conda-based)..."
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docker build -t pocketminer:latest .
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@echo "Build complete!"
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# Run single test prediction
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run:
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@if [ ! -f test.pdb ]; then \
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echo "Error: test.pdb not found. Please provide a test PDB file."; \
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exit 1; \
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fi
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@echo "Running PocketMiner prediction on test.pdb..."
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docker run --rm \
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-v $(PWD):/data \
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pocketminer:latest \
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python /workspace/entrypoint.py \
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--pdb /data/test.pdb \
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--output-folder /data/output \
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--output-name test
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@echo "Results saved to output/"
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# Run Nextflow pipeline
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test:
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@echo "Running Nextflow pipeline..."
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nextflow run main.nf
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@echo "Pipeline complete!"
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# Clean generated files
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clean:
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@echo "Cleaning up..."
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rm -rf output/
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rm -rf .nextflow/
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rm -f .nextflow.log*
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rm -rf work/
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rm -rf results/
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rm -f *.npy *.txt
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@echo "Clean complete!"
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# Open shell in container
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shell:
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docker run --rm -it \
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-v $(PWD):/data \
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pocketminer:latest \
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/bin/bash
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# Download example PDB (if internet available)
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download-example:
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@echo "Downloading example PDB (1HSG - HIV protease)..."
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wget -O test.pdb https://files.rcsb.org/download/1HSG.pdb
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@echo "Example downloaded as test.pdb"
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