IRIDA Snippy Phylogenomics Pipeline Plugin

This project contains a pipeline implemented as a plugin for the IRIDA bioinformatics analysis system. This can be used to call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.

Table of Contents

• IRIDA Snippy Phylogenomics Pipeline Plugin
• Installation
  • Installing Galaxy Dependencies
  • Installing to IRIDA
• Usage
  • Analysis Results
  • Metadata Table
• Building
  • Installing IRIDA to local Maven repository
  • Building the plugin
• Dependencies

Installation

Installing Galaxy Dependencies

In order to use this pipeline, you will also have to install the following Galaxy tools and data managers within your Galaxy instance. These can be found at:

Name	Version	Owner	Metadata Revision	Galaxy Toolshed Link
snippy	4.4.5	iuc	10 (2020-01-30)	snippy-10:3fe8ef358d66
gubbins	2.2.1	iuc	0 (2017-06-23)	gubbins-0:637ec5d5368c
snp_sites	2.5.1	iuc	1 (2019-11-02)	snp_sites-1:5804f786060d
iqtree	1.5.5.3	iuc	4 (2020-04-03)	iqtree-4:f97743d52b87

NOTE: There is currently an unresolved issue in snippy involving a problem resolving the correct version number for samtools. This issue arises when snippy is installed from bioconda, as is normally the case when installing to galaxy. The issue can be resolved by:

1. Activating the conda environment where snippy was installed (this will likely be a 'mulled' environment, since the snippy galaxy tool wrapper references multiple tool dependencies.
2. Running conda install --override-channels -c conda-forge -c bioconda -c defaults samtools=1.9 to downgrade samtools.

Installing to IRIDA

Please download the provided irida-plugin-snippy-phylogenomics-[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.

Usage

The plugin should now show up in the Analyses > Pipelines section of IRIDA.

Analysis Results

You should be able to run a pipeline with this plugin and get analysis results.

Metadata Table

This pipeline plugin does not currently write any data to the IRIDA Metadata Table. Future versions of this pipeline plugin will do so.

Field Name	Description

Building

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 19.01.3.

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 19.01.3

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-tetyper

mvn clean package

Once complete, you should end up with a file target/irida-plugin-snippy-phylogenomics.jar which can be installed as a plugin to IRIDA.

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)