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.
- 🔑 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
This package is not yet on CRAN. Install directly from GitHub:
# install.packages("remotes")
remotes::install_github("JulFrey/GalaxyR")Before using the package, you must set your Galaxy API key.
You can either:
galaxy_set_credentials("your-secret-key")#usethis::edit_r_environ()
GALAXY_API_KEY = your-secret-key
Restart R after editing.Renviron.
The default Galaxy instance is:
https://usegalaxy.eu
Most functions accept a galaxy_url argument if you want to target a different Galaxy server.
Below is a complete example that:
- Creates a new history
- Uploads a text file
- Runs the “Add line to file” tool
- Waits for the job to complete
- 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])-
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)
Galaxy jobs and datasets are asynchronous.
This package provides helpers to wait safely until execution finishes:
galaxy_wait_for_job()— waits for tool executiongalaxy_wait_for_dataset()— waits for dataset processing
Terminal states: - ✅ ok - ❌ error - 🗑️ deleted
| Function | Description |
|---|---|
galaxy_initialize() |
Create a new history |
galaxy_upload_https() |
Upload a file via HTTPS |
galaxy_run_tool() |
Run a Galaxy tool |
galaxy_wait_for_job() |
Wait for job completion |
galaxy_download_result() |
Download dataset |
galaxy_get_tool() |
Inspect tool metadata |
galaxy_list_tools() |
List installed tools |
galaxy_history_size() |
Compute history disk usage |
Author:
Julian Frey
Chair of Forest Growth and Dendroecology
University of Freiburg