galaxy-bridge
Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions
npx skills add BioTender-max/awesome-bio-agent-skills --skill galaxy-bridge --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Galaxy Bridge **ClawBio's gateway to the Galaxy ecosystem — 1,770+ production bioinformatics tools, discoverable and executable through natural language.** ## Why This Exists Galaxy (usegalaxy.org) hosts the world's largest collection of curated bioinformatics tools — 1,770+ on the main server alone, covering everything from FASTQ QC to metagenomics to protein structure prediction. But discovering the right tool requires knowing exact tool IDs, navigating nested ToolShed categories, and understanding parameter schemas. Galaxy Bridge makes these tools **agent-accessible**: search by natural language, execute via CLI, and chain Galaxy tools with ClawBio's local skills for cross-platform workflows that neither system can do alone. ## Core Capabilities 1. **Intelligent tool recommendation** — describe a task in plain English; multi-signal scoring across 7 dimensions returns the best Galaxy tool with explanations 2. **Workflow suggestions** — 8 pre-defined pipeline templates (RNA-seq DE, metagenomics, variant calling, WES germline, ChIP-seq, nanopore, genome assembly, variant annotation) 3. **Input format awareness** — provide your file extension (.fastq, .bam, .vcf) for format-aware
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Recommendation Engine
- Demo
- Galaxy Tool Categories
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Intelligent tool recommendation (new in v0.2.0) python galaxy_bridge.py --recommend "quality control on my sequencing reads" python galaxy_bridge.py --recommend "classify microbial species" --format .fastq python galaxy_bridge.py --recommend "call variants" --format .bam python galaxy_bridge.py --recommend "annotate variants from WES" --format .vcf Workflow / pipeline suggestions (new in v0.2.0) python galaxy_bridge.py --workflow "RNA-seq differential expression" python galaxy_bridge.py --workflow "metagenomics" python galaxy_bridge.py --workflow "whole exome sequencing" Search for tools by keyword
What does the galaxy-bridge skill do?
Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill galaxy-bridge --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.