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Geneious Plugin

Dave O'Connor's Laboratory at the University of Wisconsin-Madison developed a custom Geneious Prime plugin that allows TaxTriage analyses to be run directly from within the Geneious bioinformatics platform - no command-line knowledge required.

The plugin integrates with Docker and Nextflow to execute the full TaxTriage workflow, accepting file inputs through Geneious's GUI and importing results back into the project.

Prerequisites

Required Software

  • Geneious Prime version 2024.0.2 or later
  • Docker - must be installed and running on your system
  • Nextflow - pulled automatically via Docker on first run
  • TaxTriage databases - downloaded automatically by the workflow on first run

Installation

  1. Locate the TaxTriage.gplugin file in the repository:
src/geneious-plugin/TaxTriage.gplugin

This file is built for macOS ARM (Apple Silicon). It may work on Windows/Linux but has not been officially tested on those platforms.

  1. Copy it to your Geneious plugins directory:
OS Path
macOS ~/.geneious/plugins/
Windows %USERPROFILE%\.geneious\plugins\
Linux ~/.geneious/plugins/
  1. Restart Geneious.

Usage

Launch TaxTriage

Go to Tools > TaxTriage Analysis in Geneious.

Select Input Files

Choose one of:

  • Input Files - Click "Browse" to select individual FASTQ/FASTA files
  • Input Directory - Click "Browse" to select a folder of sequence files

Configure Sequencing Preset

Preset Use For
ONT (Oxford Nanopore) Long-read sequencing data
Illumina PE Paired-end Illumina reads
Illumina SE Single-end Illumina reads

Quality Parameters

Set minimum quality thresholds for filtering (equivalent to --minq).

Run the Analysis

Click Run to start the pipeline. The plugin generates a configuration file, launches Docker + Nextflow, and runs the TaxTriage workflow.

Results are imported back into Geneious upon completion.

Building the Plugin from Source

Prerequisites

  • Java 11 or higher
  • Apache Ant
  • Geneious devkit (for API dependencies)

Project Structure

src/geneious-plugin/
├── src/                  # Java source code
│   └── com/jhuapl/taxtriage/geneious/
├── test/                 # Unit tests
├── lib/                  # Required JARs
│   ├── GeneiousPublicAPI.jar
│   ├── jdom.jar
│   └── jebl.jar
├── resources/
│   ├── presets/          # Analysis presets
│   └── templates/        # Configuration templates
├── plugin.properties     # Plugin metadata
├── build.xml             # Ant build script
└── README.md

Dependencies

Dependency Purpose
GeneiousPublicAPI.jar Core Geneious plugin API
jdom.jar XML document processing
jebl.jar Java Evolutionary Biology Library

These JARs are automatically copied from the Geneious devkit during project setup.

Build Commands

From the src/geneious-plugin/ directory:

# Set up the project (copies devkit JARs)
ant setup

# Build the plugin
ant build

# Run unit tests
ant test

# Package the .gplugin file
ant package

The resulting TaxTriage.gplugin will be in build/.

Docker Integration

The plugin handles Docker automatically. On first run:

  1. The Nextflow Docker image is pulled
  2. TaxTriage container images are pulled
  3. Databases are downloaded to the working directory

For details on the Docker integration architecture, see src/geneious-plugin/docs/DOCKER_INTEGRATION.md in the repository.

Support and Compatibility

  • Tested on: macOS ARM (Apple Silicon) with Geneious Prime 2024.0.2+
  • Untested on: Windows, Linux (may work but not officially supported)
  • For issues with the plugin, open a GitHub issue or contact the development team.