IRIDA Plasmid Screen Pipeline Plugin

Table of Contents

• IRIDA Plasmid Screen Pipeline Plugin
• Installation
  • Installing to IRIDA
  • Installing Galaxy Dependencies
  • Setting up your abricate report screening file(s)
• Usage
  • Monitoring Pipeline Status
  • Analysis Results
  • Metadata Table
• Building
  • Installing IRIDA Libraries
  • Building Plasmid-Screen Plugin

Installation

Installing to IRIDA

Please download the provided irida-plugin-plasmid-screen-[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
unicycler	0.4.8	iuc	7 (2019-10-08)	unicycler-7:88c240872a65
quast	5.0.2	iuc	5 (2018-12-04)	quast-5:81df4950d65b
mob_suite	2.0.5	nml	6 (2019-12-11)	mob_suite-6:9424de64bfa8
abricate	0.9.8	iuc	7 (2019-10-29)	abricate-7:4efdca267d51
pick_plasmids_containing_genes	0.2.0	public-health-bioinformatics	1 (2019-12-19)	pick_plasmids_containing_genes-1:c9129ecc609d
screen_abricate_report	0.4.0	public-health-bioinformatics	4 (2020-01-03)	screen_abricate_report-4:22247b1a59d5
collapse_collections	4.1	nml	5 (2019-08-27)	collapse_collections-5:33151a38533a
combine_tabular_collection	0.1	nml	0 (2017-02-06)	combine_tabular_collection-0:b815081988b5
bundle_collections	1.2.1	nml	1 (2017-08-04)	bundle_collections-1:cd6da887a5f4
text_processing	(multiple)	bgruening	13 (2019-04-03)	text_processing-13:0a8c6b61f0f4

Setting up your abricate report screening file(s)

Abricate report screening files have a simple tabular format, and can be created with Excel, another spreadsheet application, or a plaintext editor. They consist of two columns, with headings gene_name and regex. All fields must be tab-delimited.

gene_name    regex
KPC          ^KPC-\d+$
OXA          ^OXA-\d+$
NDM          ^NDM-\d+$

Preparing the 'abricate_report_screening_files' Tool Data Table in Galaxy

This workflow requires that the abricate report screening files described above are made available via a Galaxy Tool Data Table called abricate_report_screening_files. We recommend that you use the data_manager_manual tool to manage that data table.

Usage

Monitoring Pipeline Status

To monitor the status of the launched pipeline, please select the Analyses > Your Analyses menu.

From here, you can monitor the status of your pipeline.

Analysis Results

Once the analysis pipeline is finished, you can view the analysis results in your browser or download the files to your machine.

These results include ...

Metadata Table

If you selected the Save Results to Project Line List Metadata option when launching the pipeline...

Building

Installing IRIDA Libraries

To build this plugin yourself, you must first install IRIDA to your local Maven repository. Please make sure you are installing the IRIDA version defined in the irida.version.compiletime property in the pom.xml file (e.g., 19.01.3). Or, alternatively, please update the IRIDA dependency version in the pom.xml file.

To install the IRIDA libraries to a local Maven repository, please run the following from within the IRIDA project (the irida/ directory):

mvn clean install -DskipTests

Building the Plugin

Once IRIDA is installed, you may build the pipeline plugin by running the following in this project's directory (the irida-plugin-plasmid-screen directory):

mvn clean package

This should produce a target/*.jar file, which can be copied into /etc/irida/plugins/.