galaxy-bridge

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 recommendations
4. Version deduplication — 8,182 catalog entries collapse to ~2,300 unique tools; latest version preferred, version count as maturity signal
5. EDAM ontology resolution — 108 EDAM topic/operation IDs resolved to human-readable labels for richer matching
6. Natural language search — keyword-based search across 8,000+ Galaxy tools by name, description, section, and EDAM terms
7. Remote execution — run Galaxy tools on usegalaxy.org via BioBlend API
8. Category browsing — explore 86 ToolShed categories with tool counts
9. Tool detail inspection — view inputs, outputs, and parameter schemas
10. Offline demo mode — FastQC demo with pre-cached results (no API key needed)
11. Cross-platform chaining — Galaxy VEP → ClawBio PharmGx, Galaxy Kraken2 → ClawBio metagenomics

Input Formats

Format	Extension	Required Fields	Example
FASTQ	.fq, .fastq, .fq.gz	Sequence reads	Illumina paired-end reads
VCF	.vcf, .vcf.gz	Variant calls	Annotated VCF for VEP
BAM	.bam	Aligned reads	BWA-MEM2 output
FASTA	.fa, .fasta	Sequences	Reference genome
Tabular	.tsv, .csv	Varies by tool	Gene expression matrix