IRIDA MLST Pipeline Plugin

Table of Contents

• IRIDA MLST Pipeline Plugin
• Installation
  • Installing to IRIDA
  • Installing Galaxy Dependencies
• Usage
  • Monitoring Pipeline Status
  • Analysis Results
  • Metadata Table
• Building
  • Installing IRIDA Libraries
  • Building MLST Plugin

Installation

Installing to IRIDA

Please download the provided irida-plugin-mlst-[version].jar from the releases page and copy to your /etc/irida/plugins directory. Now you may start IRIDA and you should see the pipeline appear in your list of pipelines.

Note: This plugin requires you to be running IRIDA version >= 19.01. Please see the IRIDA documentation for more details.

Installing Galaxy Dependencies

In order to use this pipeline, you will also have to install the mlst, quast, and shovill (for assembly) Galaxy tools within your Galaxy instance. These can be found at:

Name	Version	Galaxy Tool
mlst	2.16.1	https://toolshed.g2.bx.psu.edu/view/iuc/mlst/1f5641a52664
quast	5.0.2	https://toolshed.g2.bx.psu.edu/view/iuc/quast/81df4950d65b
shovill	1.0.4	https://toolshed.g2.bx.psu.edu/view/iuc/shovill/865119fcb694

Usage

Monitoring Pipeline Status

To monitor the status of the launched pipeline, please select the Analyses > Your Analyses menu.

From here, you can monitor the status of your pipeline.

Analysis Results

Once the analysis pipeline is finished, you can view the analysis results in your browser or download the files to your machine.

These results include the MLST profile as generated by mlst, and a summary of the quality of the assembly generated by shovill. The assembly quality summary is generated by quast.

Metadata Table

If you selected the Save Results to Project Line List Metadata option when launching the pipeline, the MLST scheme and sequence type will be integrated into the IRIDA Line List/Metadata table as shown below.

Building

Installing IRIDA Libraries

To build this plugin yourself, you must first install IRIDA to your local Maven repository. Please make sure you are installing the IRIDA version defined in the irida.version.compiletime property in the pom.xml file (e.g., 19.01.3). Or, alternatively, please update the IRIDA dependency version in the pom.xml file.

To install the IRIDA libraries to a local Maven repository, please run the following from within the IRIDA project (the irida/ directory):

mvn clean install -DskipTests

Building MLST Plugin

Once IRIDA is installed, you may build the pipeline plugin by running the following in this project's directory (the irida-plugin-mlst/ directory):

mvn clean package

This should produce a target/*.jar file, which can be copied into /etc/irida/plugins/.