NEWS.md

In GalaxyR: 'Galaxy' API Implementation

GalaxyR 0.1.2

• Add galaxy_list_files function to list all files from an existing history
• Add functionality to delete/purge histories
• Add print function for tool parameters/options
• Add a small reproducible example from genomics

GalaxyR 0.1.1

• Add support to download full histories i.e. as RO-CRATE by adding the galaxy_download_rocrate() function.

GalaxyR 0.1.0 (Initial CRAN release)

• Initial release of the Galaxy R client, providing a high-level and S4-based interface to Galaxy’s REST API. S4 Galaxy session object to carry state (history, datasets, invocation IDs, outputs, status) through pipe-based workflows.
• Supports configuring Galaxy connection parameters via environment variables (GALAXY_API_KEY, GALAXY_URL) and helper galaxy_initialize() constructor.
• History management: list histories, create new histories, inspect history sizes (robust to different Galaxy size fields), and include deleted items optionally.
• Dataset operations: upload via HTTPS (and FTP helper), wait for completion, retrieve dataset metadata, download results with safe/unique file naming, and delete single or multiple datasets with optional purge.
• Workflow operations: list workflows (including published), fetch workflow metadata and inputs, start workflow invocations, and poll workflow execution with job-level state tracking and result collection.
• Tooling: list tools (with optional panel filtering), fetch detailed tool definitions, validate tool inputs, and run single tools with automatic dataset input wiring.

GalaxyR documentation built on July 6, 2026, 5:08 p.m.