Agent skill · software engineering · delphine-l
galaxy-automation
BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking, error handling, batch processing, and dataset management. Essential for any Galaxy automation project.
Why this skill is useful
Adds executable scripts and detailed patterns for Galaxy automation that are not commonly found in public documentation.
What it needs
Requires bioblend, planemo installed locally. About 4k tokens when loaded. Last updated 2026-05-14. 17 stars on the source repository.
What this skill does
Galaxy Workflow Automation with BioBlend and Planemo Purpose This skill provides expert knowledge for automating Galaxy workflows using BioBlend (Python Galaxy API library) and Planemo (Galaxy workflow testing and execution tool). When to Use This Skill Use this skill when: Automating Galaxy workflow execution via API Building batch processing systems for Galaxy Using BioBlend to interact with Galaxy Testing workflows with Planemo Managing Galaxy histories, datasets, and collections programmatically Polling workflow invocation status Implementing error handling and retry logic for Galaxy operations Creating Galaxy automation pipelines Integrating Galaxy into larger bioinformatics workflows This skill is NOT project-specific - it's useful for ANY Galaxy automation project. Supporting Files Detailed reference material is split into separate files: bioblend-reference.md -- BioBlend API patterns: connection, history management, workflow invocation, status checking, error handling, rerun API, dataset operations, and collections planemo-reference.md -- Planemo command structure, job YAML format, programmatic command generation, output parsing, and Galaxy API curl/authentication patterns automation-patterns.md -- Thread-safe operations, batch processing, resume capability, and debugging (history inspection, invocation step analysis) --- Security Best Practices 1. API Key Management Store in environment variables: Mask in logs: --- 2. Path Handling Always quote paths in shell commands: --- Common Pitfalls 1. Planemo failures vs Galaxy failures Planemo return code != 0: Workflow was NOT launched, no invocation exists Invocation state = 'failed': Workflow was launched but Galaxy job failed Don't confuse these two failure modes 2. Concurrent uploads Too many simultaneous uploads can overwhelm Galaxy Use maxconcurrent limits (typically 3-5) Consider --simultaneousuploads vs sequential 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills delphine-l/automation