IRIDAPlugin Dev Doc

Step by step handson doc for anyone who wants to develop new plugin for IRIDA

Plugin Overview

Prerequisite

IRIDA - Locally Installed

https://phac-nml.github.io/irida-documentation/developer/tools/pipelines/#4-test-in-irida:~:text=is%20as%20follows.-,3.2.1.%20Install%20IRIDA%20to%20local%20Maven%20repository,-In%20order%20to

Also, download the example-plugin

https://phac-nml.github.io/irida-documentation/developer/tools/pipelines/#4-test-in-irida:~:text=publishToMavenLocal%20%2Dxtest-,3.2.2.%20Download%20IRIDA%20plugin%20example,-Once%20you%E2%80%99ve%20installed

Galaxy - Locally Installed

1. Install the tool in Galaxy (SeroTypeFinder)
2. Create galaxy workflow for SeroTypeFinder

3. Input box should be "list:paired" and the name should be "sequence_reads_pair"

• Test the workflow to make sure it produces the expected output
• Rename the output files and change data type also
• Export the workflow

Converting Galaxy workflow to IRIDA plugin

• cd /home/irida/
• git clone https://github.com/phac-nml/irida-plugin-example
• change name mv irida-plugin-example/ serotypefinder/
• cd serotypefinder/

IRIDA provides a java file to create the templates (information and XML files) for the plugin development

• https://github.com/phac-nml/irida-wf-ga2xml/releases
• git clone https://github.com/phac-nml/irida-wf-ga2xml/releases#:~:text=irida%2Dwf%2Dga2xml%2D1.2.1%2Dstandalone.jar

java -jar irida-wf-ga2xml-1.2.1-standalone.jar -n SeroTypeFinder -t SeroTypeFinder -W 1.0.0 -o output -i Galaxy-Workflow-SerotyperFinder.ga

• Results are stored in output/ folder
• Copy the outputs cp output/SeroTypeFinder/1.0.0/* serotyper/src/main/resources/workflows/1.0.0/
• Directories which are important:
  • galaxy Workflow, plugin information and XML files serotyper/src/main/resources/workflows/
  • Java files /src/main/java/ca/corefacility/bioinformatics/irida/plugins/
• Change java file names
  • cd /src/main/java/ca/corefacility/bioinformatics/irida/plugins/
  • mv ExamplePlugin.java SeroTypeFinderPlugin.java
  • mv ExamplePluginUpdater.java SeroTypeFinderPluginUpdater.java
    
    
• Edit the src/main/resources/workflows/1.0.0/messages_en.properties file
  https://github.com/NorwegianVeterinaryInstitute/irida-nvi-serotypefinder/blob/main/src/main/resources/workflows/1.0.0/irida_workflow.xml
  
  
• Edit the src/main/resources/workflows/1.0.0/messages_en.properties file
  https://github.com/NorwegianVeterinaryInstitute/irida-nvi-serotypefinder/blob/main/src/main/resources/workflows/1.0.0/messages_en.properties
  
  
• Edit the serotypefinder/pom.xml file
  https://github.com/NorwegianVeterinaryInstitute/irida-nvi-serotypefinder/blob/main/pom.xml

* Edit the ```SeroTypeFinderPlugin.java```
https://github.com/NorwegianVeterinaryInstitute/irida-nvi-serotypefinder/blob/main/src/main/java/ca/corefacility/bioinformatics/irida/plugins/SeroTypeFinderPlugin.java

* Edit the ```SeroTypeFinderPluginUpdater.java```
https://github.com/NorwegianVeterinaryInstitute/irida-nvi-serotypefinder/blob/main/src/main/java/ca/corefacility/bioinformatics/irida/plugins/SeroTypeFinderPluginUpdater.java

Build the plugin

• mvn clean package
• check the target/folder for SeroTypeFinder-1.0.0.jar file
• Transfer the file to /etc/irida/plugins/in IRIDA VM
• Restart the tomcat