GalaxyR

Description

GalaxyR is an R package for programmatic interaction with the Galaxy API (tested primarily against Galaxy Europe).
It allows you to manage histories, upload data, run tools and workflows, wait for jobs to complete, and download results — all directly from R.

This package is designed for automation, reproducibility, and scripting, not UI replacement.

Features

• 🔑 Simple API key management
• 📁 Create and manage Galaxy histories
• ⬆️ Upload datasets via HTTPS or FTP
• 🔧 Discover and inspect Galaxy tools and workflows
• ▶️ Run tools and workflow programmatically
• ⏳ Wait for jobs to finish (robust polling)
• 📥 Download resulting datasets
• 📊 Inspect history size and disk usage
• 🔧 S4-based interface for pipe friendly usage

Installation

This package is not yet on CRAN. Install directly from GitHub:

# install.packages("remotes")
remotes::install_github("JulFrey/GalaxyR")

Authentication

Before using the package, you must set your Galaxy API key.

You can either:

Option 1: Set it once per session

galaxy_set_credentials("your-secret-key")

Option 2: Add it to ~/.Renviron (recommended)

#usethis::edit_r_environ()
GALAXY_API_KEY = your-secret-key

Restart R after editing.Renviron.

Supported Galaxy Instances

The default Galaxy instance is:

https://usegalaxy.eu

Most functions accept a galaxy_url argument if you want to target a different Galaxy server.

Basic Workflow Example

Below is a complete example that:

1. Creates a new history
2. Uploads a text file
3. Runs the “Add line to file” tool
4. Waits for the job to complete
5. Downloads and inspects the result

# Get the tool ID and inspect inputs 
tool <- galaxy_get_tool_id("Add line to file")
inputs <- galaxy_get_tool(tool)

# Create a tiny test file
test_file <- tempfile(fileext = ".txt")
test_text <- "This is an example \ntest file."
writeLines(test_text,test_file)

# directory for outputs
outdir <- tmp_dir()

# Run on Galaxy
gxy <- galaxy(history_name = "add line example") |> # S4 class with history name
  galaxy_initialize() |> # initialise Galaxy history
  galaxy_upload_https(test_file) |> # upload test file
  galaxy_run_tool(tool, inputs = list(text_input = "added example text")) |> # run 
  galaxy_poll_tool() |> # wait for compleation
  galaxy_download_result(outdir)

# Inspect the result
readLines(list.files(outdir)[1])

Important Notes on Tool Inputs

• Always use input name, not label
  Example: text_input, not "text to add"

• Dataset inputs must be passed as objects, not plain strings:

  infile = list(
    src = "hda",
    id  = DATASET_ID
  )

• You can inspect expected inputs using:

  galaxy_get_tool(tool_id)

Job and Dataset States

Galaxy jobs and datasets are asynchronous.

This package provides helpers to wait safely until execution finishes:

• galaxy_wait_for_job() — waits for tool execution
• galaxy_wait_for_dataset() — waits for dataset processing

Terminal states: - ✅ ok - ❌ error - 🗑️ deleted

Common Helper Functions

Author:
Julian Frey
Chair of Forest Growth and Dendroecology
University of Freiburg