openbiomcp 0.1.1

BioOpenMCP: Model Context Protocol tools and CLI for bioinformatics workflows.

OpenBioMCP

OpenBioMCP is a Python package for running Model Context Protocol (MCP) tools, including FastQC integration and other bioinformatics utilities with comprehensive background execution and status checking capabilities.

Installation

pip install openbiomcp

MCP Configuration

After installation, you need to configure the MCP server in Claude Desktop:

Step 1: Find the installation path

Mac:

which openbiomcp

Example output: /opt/anaconda3/bin/openbiomcp

Windows:

where openbiomcp

Copy the path from the output.

Step 2: Configure Claude Desktop

Add the following configuration to your Claude Desktop settings:

{
  "mcpServers": {
    "BioOpenMCP": {
      "command": "<PATH>"
    }
  }
}

Example for Mac:

{
  "mcpServers": {
    "BioOpenMCP": {
      "command": "/opt/anaconda3/bin/openbiomcp"
    }
  }
}

Replace <PATH> with the actual path from Step 1.

Step 3: Restart Claude Desktop

After adding the configuration, restart Claude Desktop to load the MCP server.

Features

• Modular design - Organized by feature/domain for scalability
• Background execution - Run long-running bioinformatics tools without blocking
• Real-time status monitoring - Check job progress and retrieve results
• Job management - Start, stop, and clean up background jobs
• CLI entry point - Command-line interface for easy access
• MCP integration - Expose tools through Model Context Protocol
• Ready for PyPI distribution

Available Bioinformatics Tools

Tool	Purpose	Trigger Prompt Examples
FastQC	Quality control analysis for FASTQ files	"Run FastQC on my sample.fastq file" "Check the quality of my sequencing data" "Generate a quality report for sample_R1.fastq"
Cutadapt	Adapter trimming for sequencing data	"Trim adapters from my FASTQ file" "Remove adapter sequences using cutadapt" "Clean my sequencing data with adapter trimming"
Trim Galore	Automated adapter and quality trimming	"Run Trim Galore on my FASTQ file" "Quality trim my sequencing data" "Automatically trim adapters and low quality bases"
STAR Alignment	RNA-seq alignment tool	"Align my FASTQ files to the genome using STAR" "Run RNA-seq alignment with STAR" "Map my reads to the reference genome"
MultiQC	Aggregate bioinformatics analysis results	"Generate a MultiQC report for my analysis" "Summarize all my QC results" "Create a comprehensive report of my bioinformatics analysis"

Tool Categories

Quality Control

• FastQC: Comprehensive quality control analysis
• MultiQC: Aggregate and visualize QC results

Data Processing

• Cutadapt: Precise adapter trimming
• Trim Galore: Automated quality and adapter trimming

Alignment

• STAR: High-performance RNA-seq alignment
• Genome Indexing: Build STAR genome indices

Background Execution

All tools support background execution with real-time monitoring:

• Start jobs in the background
• Check job status and progress
• Retrieve results when complete
• Stop or cancel running jobs
• Clean up completed jobs