This project contains a fast phylogeny pipeline implemented as a plugin for the IRIDA bioinformatics analysis system.

Workflow

Required Galaxy tools

• toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1
• testtoolshed.g2.bx.psu.edu/repos/leomrtns/iqtree/iqtree/1.6.12

Building/Packaging

Building and packaging this code is accomplished using Apache Maven. However, you will first need to install IRIDA to your local Maven repository. The version of IRIDA you install will have to correspond to the version found in the irida.version.compiletime property in the pom.xml file of this project. Right now, this is IRIDA version 19.09-SNAPSHOT.

Installing IRIDA to local Maven repository

To install IRIDA to your local Maven repository please do the following:

1. Clone the IRIDA project

git clone https://github.com/phac-nml/irida.git
cd irida

2. Checkout appropriate version of IRIDA

git checkout 19.09-SNAPSHOT

3. Install IRIDA to local repository

mvn clean install -DskipTests

Building the plugin

Once you've installed IRIDA as a dependency, you can proceed to building this plugin. Please run the following commands:

cd irida-plugin-qi-taxon

mvn clean package

Once complete, you should end up with a file target/qi-taxon-0.1.0-SNAPSHOT.jar which can be installed as a plugin to IRIDA.

If you have previously setup IRIDA before you may copy this JAR file to /etc/irida/plugins and restart IRIDA. The plugin should now show up in the Analyses > Pipelines section of IRIDA.

You should be able to run a pipeline with this plugin and get analysis results. And, you should be able to save and view these results in the IRIDA metadata table.

Dependencies

The following dependencies are required in order to make use of this plugin.

• IRIDA >= 0.23.0
• Java >= 1.8 and Maven (for building)