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galaxy-bridge

Recommend and execute Galaxy bioinformatics tools via the BioBlend API.

1.1k|238|Updated Feb 25, 2026
Search Tags:#bioinformatics#reproducibility#galaxy#tool-discovery#bioblend#workflow-recommendation#ngs
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill galaxy-bridge
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: galaxy-bridge
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/galaxy-bridge
Command: npx skills add https://github.com/ClawBio/ClawBio --skill galaxy-bridge

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Finding the right Galaxy tool and executing it on a public Galaxy server is time-consuming and error-prone: tool IDs are opaque, categories are deep, versions are duplicated, and uploading/running tools via the API requires boilerplate and reproducibility work. Galaxy-bridge centralises discovery, ranks candidate tools by multi-signal scoring, and automates execution and result retrieval so users can get reproducible outputs quickly.

Core Features & Use Cases

  • Intelligent tool recommendation: natural-language queries return ranked Galaxy tool suggestions with explanations and EDAM-derived labels.
  • Workflow suggestions: pre-defined pipeline templates (RNA-seq DE, metagenomics, WES, etc.) for multi-step analyses.
  • Remote execution: upload inputs, run tools, poll status, download outputs, and clean up histories via the BioBlend API.
  • Offline discovery & demos: bundled galaxy_catalog.json enables local search and an offline FastQC demo that works without credentials.
  • Version deduplication & provenance: collapses tool versions, prefers latest, and writes reproducibility bundles (commands.sh, environment.yml, checksums).
  • Use Case: recommend and run a QC or taxonomic-classification tool on sequencing reads, then bundle outputs for reproducibility and peer review.

Quick Start

Ask galaxy-bridge to recommend a Galaxy tool for quality control on my sequencing reads and run the demo FastQC without an API key.

Frequently Asked Questions about galaxy-bridge

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

FAQPage Schema
How do I find the right Galaxy bioinformatics tool for my sequencing reads?▼

Galaxy tool discovery uses natural-language queries to return ranked tool suggestions with EDAM-derived labels for sequencing reads. It applies multi-signal scoring to match your genomics, transcriptomics, or metagenomics workflows.

Can I run Galaxy tools remotely via the BioBlend API?▼

Yes, you can run Galaxy tools remotely via the BioBlend API using GALAXY_URL and GALAXY_API_KEY. It handles uploading inputs, running tools, polling status, downloading outputs, and cleaning up histories automatically.

Do I need an API key to test Galaxy bioinformatics tools?▼

You do not need an API key for offline discovery. A bundled galaxy_catalog.json enables local tool search and an offline FastQC demo works without credentials or remote server access.

How can I ensure reproducibility for my NGS analysis on Galaxy?▼

Reproducibility for NGS analysis is ensured by generating reproducibility bundles containing commands.sh, environment.yml, and checksums. It deduplicates tool versions and prefers the latest for provenance tracking.

Are there pre-defined workflow templates for RNA-seq differential expression?▼

Pre-defined workflow templates exist for RNA-seq differential expression, metagenomics, and whole exome sequencing. These templates provide structured pipeline steps for multi-step Galaxy bioinformatics analyses.

What is the best way to manage multiple versions of the same Galaxy tool?▼

Managing multiple Galaxy tool versions is handled by version deduplication, which collapses duplicates and prefers the latest. This simplifies tool discovery and ensures reproducible workflows.

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