IRIDA MiCall-Lite Pipeline Plugin

Genotype viral samples by iterative realignment against reference sequences.

Derived from the MiCall pipeline from the BC Centre for Excellence in HIV/AIDS Research, and MiCall-Lite from Dr. Art Poon at Western University

Table of Contents

• IRIDA MiCall-Lite Pipeline Plugin
• Installation
  • Installing to IRIDA
  • Installing Galaxy Dependencies
• Usage
  • Monitoring Pipeline Status
  • Analysis Results
  • Metadata Table
• Building/Packaging
  • Installing IRIDA to local Maven repository
  • Building the plugin
• Dependencies

Installation

Installing to IRIDA

Please download the provided irida-plugin-micall-lite-[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 several Galaxy tools within your Galaxy instance. These can be found at:

Name	Version	Owner	Metadata Revision	Galaxy Toolshed Link
micall_lite	0.1rc5+galaxy0	public-health-bioinformatics	4 (2020-02-28)	micall_lite-4:27d61a7f82f1
fastp	0.19.5+galaxy1	iuc	8 (2019-05-28)	fastp-8:1d8fe9bc4cb0

Setting up your MiCall-Lite projects.json File

MiCall-Lite requires a projects.json file that defines specific genomic regions and sequences to align against.

An example projects.json file is available on the MiCall-Lite GitHub Repo

The file is structured as follows:

{
  "projects": {
    "ERCC": {
      "max_variants": 0,
      "description": "External RNA Controls Consortium reference; https://doi.org/10.1186/1471-2164-6-150",
      "regions": [
        {
          "coordinate_region": "ERCC-00002",
          "seed_region_names": [
            "ERCC-00002-seed"
          ]
        },
        ...
        "HCV": {
              "max_variants": 0,
              "description": "Hepatitis C virus, coding regions",
              "regions": [
                {
                  "coordinate_region": "HCV1A-H77-Core",
                  "seed_region_names": [
                    "HCV-1a",
                    "HCV-1c",
                    "HCV-1e",
                    "HCV-1g"
                  ]
                },
        ...
        "HIV": {
              "max_variants": 0,
              "description": "Human immunodeficiency virus type 1, coding regions",
              "regions": [
                {
                  "coordinate_region": "GP41",
                  "seed_region_names": [
                    "HIV1B-env-seed"
                  ]
                },
        ...
        },
    "regions": {
        "ERCC-00002": {
          "is_nucleotide": false,
          "reference": [
            "PDYFHFRPSCSQYTGVGIQTVG*SWFY*ARLAYEHYGQ*FLEE*VPRKKRTFGFQSCTVALNSDR",
            "SQKNEI*AYGRSEWHKACSVSWHKIPCLDVIHVSGNCLVMRLFPGVRAAGICCKEGR*VRPTSLP",
            "PFSLLGPVSQFSEVPPYAEDHLKRASSLFVVRRLLVWRRIARIINCAVRAASEEVCCGFALTAGR",
            "RHNDSDSVSGDLHMFAAYFRWALASFRSQNRAIIPVLIYWTRNVGPSVVRIPRRLRAVYTLLSND",
            "CTTCDHLIQNYQSSSPRSGLVRTAAFARVCGL*LFSLDGLAHIWLTRRIVAIHRFARQSVLVGVR",
            "PRDSWLNGRTTRQPVLAFYP*KKKKKKK"
          ],
          "seed_group": null
        },
        ...
    }
}

Preparing the 'micall_lite_projects_files' Tool Data Table in Galaxy

This workflow requires that the MiCall-Lite projects.json files described above are made available via a Galaxy Tool Data Table called micall_lite_projects_files. We recommend that the galaxy administrator use the data_manager_manual tool to manage that data table.

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 19.01.3.

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-example

mvn clean package

Once complete, you should end up with a file target/irida-plugin-micall-lite-<version>.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.

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)

6. Distribute

Once you've successfully built your plugin, you can distribute the JAR file to other IRIDA users to install in their instances.