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MubasherMohammed
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galaxy-bridge

Discover and execute Galaxy bioinformatics tools via the BioBlend API.

Updated May 10, 2026
Search Tags:#bioinformatics#genomics#tool discovery#workflows#galaxy#proteomics#metagenomics#ngs
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill galaxy-bridge-mubashermohammed
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: galaxy-bridge
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/galaxy-bridge
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill galaxy-bridge-mubashermohammed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires bioblend, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill simplifies discovering and executing bioinformatics tools from the Galaxy platform, enabling users to leverage a vast collection of bioinformatics tools with intelligent recommendations and workflow suggestions.

Core Features & Use Cases

  • Intelligent Tool Recommendation: Search by natural language or specify an input format to receive the best tool recommendations.
  • Workflow Suggestions: Get pre-defined pipeline templates for common bioinformatics workflows.
  • Input Format Awareness: Recognize and suggest tools based on file extensions.
  • Version Deduplication: Ensure the most mature and widely used tool versions are suggested.
  • EDAM Ontology Resolution: Improve matching by resolving EDAM IDs to human-readable labels.
  • Natural Language Search: Search across 8,000+ Galaxy tools by keyword.
  • Remote Execution: Run Galaxy tools on usegalaxy.org using the BioBlend API.
  • Category Browsing: Explore ToolShed categories with tool counts.
  • Tool Detail Inspection: View inputs, outputs, and parameter schemas for any tool.
  • Offline Demo Mode: Run a simulated analysis with pre-cached results without needing an API key.
  • Cross-platform Chaining: Chain Galaxy tools with ClawBio's local skills for integrated workflows.
  • Use Case: Need to analyze a metagenomic sample? Use the Skill to search for relevant tools, choose a workflow, and execute the analysis in a streamlined process.

Quick Start

Run the galaxy-bridge skill to get recommendations for tools to analyze metagenomic data.

Frequently Asked Questions about galaxy-bridge

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I discover and execute bioinformatics tools from the Galaxy platform?▼

You can discover and execute Galaxy bioinformatics tools by searching with natural language or input file formats. This process provides intelligent tool recommendations, workflow suggestions, and remote execution capabilities via the BioBlend API on usegalaxy.org.

Can I search for Galaxy metagenomics and proteomics tools using natural language?▼

Yes, you can search across 8,000+ Galaxy bioinformatics tools using natural language keywords. It matches your query to relevant tools for metagenomics, proteomics, and genomics while deduplicating versions to suggest the most mature options.

Do I need an API key to test Galaxy tool recommendations and workflows?▼

No, you do not need an API key to test Galaxy tool recommendations. You can use the offline demo mode to run simulated bioinformatics analyses with pre-cached results before connecting to the live Galaxy API.

What is the best way to chain local bioinformatics scripts with remote Galaxy workflows?▼

The best way to chain local scripts with remote Galaxy workflows is by using cross-platform chaining. This integrates Galaxy tools with local skills, allowing you to discover tools, execute them remotely, and process outputs locally.

How does EDAM ontology resolution improve bioinformatics tool discovery?▼

EDAM ontology resolution improves bioinformatics tool discovery by resolving EDAM IDs to human-readable labels. This enhances search matching accuracy when you specify input formats or browse ToolShed categories for genomics workflows.

Can I view parameter schemas and input formats for Galaxy NGS tools before execution?▼

Yes, you can inspect tool details to view inputs, outputs, and parameter schemas for any Galaxy NGS tool before execution. This input format awareness ensures you select the correct bioinformatics tool for your sample data.

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