bio-mcp/bio-mcp-bedtools

bio-mcp-bedtools

MCP (Model Context Protocol) server for genome arithmetic and interval operations.

Overview

This MCP server provides access to bedtools functionality, allowing AI assistants to perform genome arithmetic operations on genomic intervals.

Features

• Genome arithmetic operations (intersect, union, merge, etc.)
• Support for BED, GFF, VCF, and other genomic formats
• File size limits and timeout protection
• Temporary file management
• Async execution with proper error handling

Installation

Using pip

pip install bio-mcp-bedtools

From source

git clone https://github.com/bio-mcp/bio-mcp-bedtools
cd bio-mcp-bedtools
pip install -e .

Configuration

Configure your MCP client (e.g., Claude Desktop) by adding to your configuration:

{
  "mcp-servers": {
    "bio-bedtools": {
      "command": "python",
      "args": ["-m", "bio_mcp_bedtools"]
    }
  }
}

Environment Variables

• BIO_MCP_MAX_FILE_SIZE: Maximum input file size (default: 100MB)
• BIO_MCP_TIMEOUT: Command timeout in seconds (default: 300)
• BIO_MCP_BEDTOOLS_PATH: Path to bedtools executable

Usage

Once configured, the AI assistant can use the following tools:

bedtools_intersect

Find overlapping intervals between two BED/GFF/VCF files

Parameters:

• input_file_a (required): Path to first input file
• input_file_b (required): Path to second input file
• write_a: Write the original entry in A for each overlap
• write_b: Write the original entry in B for each overlap

Example:

Find intersections between regions.bed and annotations.gff

Development

Running tests

pytest tests/

Building Docker image

docker build -t bio-mcp-bedtools .

License

MIT License