skills.rest
Delphine-L
Delphine-LCOMMUNITY
Explore all skills by this author →
GitHub

galaxy-automation

Automate Galaxy workflow execution and management via BioBlend and Planemo APIs.

17|2|Updated Dec 20, 2025
Search Tags:#automation#workflow#bioinformatics#galaxy#galaxy-api#planemo#bioblend
One-click install
npx skills add https://github.com/Delphine-L/claude_global --skill galaxy-automation
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: galaxy-automation
Source: https://github.com/Delphine-L/claude_global/tree/main/skills/galaxy/automation
Command: npx skills add https://github.com/Delphine-L/claude_global --skill galaxy-automation

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires bioblend, planemo.

What problem does it solve?

This Skill provides expert tooling and knowledge to automate Galaxy workflows using BioBlend (Galaxy API) and Planemo, enabling programmatic workflow invocation, dataset management, and status tracking.

Core Features & Use Cases

  • API-driven workflow invocation: Launch Galaxy workflows and monitor their progress from a script or CI.
  • Batch processing: Run multiple workflow invocations across histories and datasets in parallel with controlled concurrency.
  • Error handling & retries: Detect failed invocations and automatically retry with configurable parameters.
  • Use Case: Automate the processing of dozens of sample datasets by invoking a single workflow across all inputs and collecting results in a report.

Quick Start

Install dependencies with pip: pip install bioblend planemo. Then create a Galaxy connection using GalaxyInstance(url="https://usegalaxy.org", key="YOUR_API_KEY") and run a simple workflow invocation via the API or Planemo. Replace URL and key with your credentials.

You can expand this setup to batch process multiple histories, datasets, and workflows.

Frequently Asked Questions about galaxy-automation

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate Galaxy workflow execution with BioBlend and Planemo?▼

Automate Galaxy workflows by installing BioBlend and Planemo, then use GalaxyInstance to connect to your Galaxy server with an API key. BioBlend provides programmatic workflow invocation, dataset management, and status tracking; Planemo handles workflow testing and execution. Configure your Galaxy URL and credentials, then invoke workflows and monitor progress via the API.

Can I batch process multiple datasets across Galaxy histories?▼

Yes. BioBlend supports batch processing by invoking a single workflow across multiple histories and datasets with controlled concurrency. Run multiple workflow invocations in parallel, track each invocation's status, and collect results. This approach scales to dozens of sample datasets without manual intervention.

What error handling and retry mechanisms does Galaxy workflow automation support?▼

BioBlend and Planemo implement configurable error handling and automatic retries for failed workflow invocations. Detect failed runs via status polling, retry with parameterized limits, and apply robust error handling throughout your automation pipeline. This ensures reliable batch processing across large datasets.

Do I need API keys to automate Galaxy workflows?▼

Yes. Galaxy automation requires an API key for authentication and a Galaxy URL to establish a GalaxyInstance connection. The API key grants programmatic access to invoke workflows, manage datasets, and query history and execution status across your Galaxy instance.

Can I integrate Galaxy workflow automation into CI/CD pipelines?▼

Yes. BioBlend and Planemo enable API-driven workflow invocation from scripts and CI systems. Launch workflows, monitor their progress, and collect results programmatically, making Galaxy automation suitable for continuous integration, batch reporting, and automated sample processing pipelines.

What's the difference between using BioBlend and Planemo for workflow automation?▼

BioBlend is the Galaxy Python API library for programmatic workflow invocation, dataset management, and history tracking. Planemo is a command-line tool for workflow development, testing, and execution. Use both together: Planemo for workflow validation and testing, BioBlend for production automation and batch processing.

Related Skills

Explore More Data & Analytics Skills→
galaxyprojectgalaxyproject
7

galaxy-integration

Automate Galaxy tool discovery, .ga validation, and workflow testing via BioBlend and MCP.

Official
Intermediate
ojowwalker77ojowwalker77
110

Matrix List

Display Matrix memory status and export recent solutions as JSON.

Community
Intermediate
Delphine-LDelphine-L
17

galaxy-tool-wrapping

Create, validate, and debug Galaxy XML tool wrappers with Planemo.

Community
Advanced
tassiovaletassiovale
13

latchbio-integration

Automate bioinformatics workflow creation and deployment using the Latch SDK.

Community
Advanced