galaxy-bridge

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.