Galaxy Bridge¶
Search, inspect, and run tools on a Galaxy server (usegalaxy.org) from the ClawBio CLI. Browse tool categories, view tool details, and execute NGS workflows without leaving your terminal.
Quick Demo¶
CLI Reference¶
# Search for tools
python3 skills/galaxy-bridge/galaxy_bridge.py \
--search "metagenomics profiling"
# List tool categories
python3 skills/galaxy-bridge/galaxy_bridge.py \
--list-categories
# Get tool details
python3 skills/galaxy-bridge/galaxy_bridge.py \
--tool-details <tool_id>
# Run a tool
python3 skills/galaxy-bridge/galaxy_bridge.py \
--run <tool_id> \
--input <file> \
--output <dir>
# Demo mode (offline FastQC example)
python3 skills/galaxy-bridge/galaxy_bridge.py --demo
| Argument | Required | Description |
|---|---|---|
--search |
No | Search Galaxy toolshed by keyword |
--list-categories |
No | List all available tool categories |
--tool-details |
No | Show full details for a tool ID |
--run |
No | Execute a Galaxy tool by ID |
--input |
No | Input file for tool execution |
--output |
No | Output directory for results |
--demo |
No | Run offline FastQC demo |
Output¶
- Search results with tool IDs, descriptions, and versions
- Tool detail pages with parameter schemas
- Execution results downloaded to the output directory
- Demo mode outputs a pre-cached FastQC report