BioQC-MCP
by Babajan-B
Overview
A Model Context Protocol (MCP) server for AI-assisted bioinformatics quality control analysis of sequencing data, including report generation and advanced visualization.
Installation
/full/path/to/BioQC-MCP/venv/bin/python3 /full/path/to/BioQC-MCP/src/server.pyEnvironment Variables
- PATH
- PYTHONUNBUFFERED
Security Notes
The `run_qc_pipeline` tool directly executes arbitrary Python code using `exec()` within a supposedly sandboxed environment (`safe_globals`). While an attempt is made to restrict the available functions, perfect sandboxing of `exec()` is notoriously difficult to achieve. This makes the server highly susceptible to arbitrary code execution if an AI agent is compromised or given a malicious prompt, leading to potential data breaches, denial-of-service, or system compromise. Subprocess calls to external tools (`fastqc`, `multiqc`) also pose a minor risk if input paths are not fully validated against path traversal attacks, though `Path().expanduser()` provides some protection.
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