JesKwek/OpenBioMCP

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 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

Usage Examples

FastQC Examples

Install FastQC

Install FastQC on my system

or

Check if FastQC is installed and install it if needed

Run FastQC in Background

Run FastQC on my sample.fastq file in the background

or

Check the quality of my sequencing data with FastQC

Check FastQC Status

Check the status of my FastQC job

or

What's the progress of my quality control analysis?

Get FastQC Results

Get the FastQC report for my analysis

or

Show me the quality control results

Cutadapt Examples

Install Cutadapt

Install cutadapt for adapter trimming

Run Cutadapt in Background

Trim adapters from my FASTQ file using cutadapt

or

Remove adapter sequences from sample.fastq

Check Cutadapt Status

Check the status of my adapter trimming job

Trim Galore Examples

Install Trim Galore

Install Trim Galore for automated trimming

Run Trim Galore in Background

Run Trim Galore on my FASTQ file

or

Quality trim my sequencing data with Trim Galore

Check Trim Galore Status

Check the status of my Trim Galore job

STAR Alignment Examples

Install STAR

Install STAR for RNA-seq alignment

Generate Genome Index

Generate a STAR genome index for my reference genome

or

Build a genome index for STAR alignment

Run STAR Alignment in Background

Align my FASTQ files to the genome using STAR

or

Run RNA-seq alignment with STAR on my data

Check STAR Status

Check the status of my STAR alignment job

MultiQC Examples

Install MultiQC

Install MultiQC for report aggregation

Run MultiQC

Generate a MultiQC report for my analysis

or

Summarize all my QC results with MultiQC

Job Management Examples

List All Jobs

Show me all running background jobs

or

List my current bioinformatics jobs

Stop a Job

Stop my FastQC job

or

Cancel my running alignment

Clean Up Jobs

Clean up completed jobs

or

Remove finished job information

Advanced Usage

Custom Parameters

Run FastQC on sample.fastq with custom parameters

Trim adapters with specific adapter sequence: AGATCGGAAGAGC

Run Trim Galore with quality threshold 20 and minimum length 50

Paired-End Analysis

Run FastQC on paired-end reads: sample_R1.fastq and sample_R2.fastq

Align paired-end RNA-seq data with STAR

Batch Processing

Run FastQC on all FASTQ files in my directory

Generate MultiQC report for all my analysis results