README.md

M. tuberculosis phylogeny IRIDA plugin

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

Using the IRIDA Builder Docker container

To build using Docker and the IRIDA Builder Docker container, run:

mkdir output
build/build_workflow.sh . output

The JAR file for the compiled pipeline will be in the output directory.

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.

Installing IRIDA to local Maven repository

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

Clone and install the IRIDA project to local repository

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

git clone https://github.com/COMBAT-TB/irida-pipeline-plugins.git
cd irida-pipeline-plugins/snippy-pipeline-plugin
mvn clean package

Once complete, you should end up with a file target/snippy-pipeline-plugin-0.1.1-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.

Dependencies

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

• IRIDA >= 19.01.1
• Java >= 1.8 and Maven (for building)