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.
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:
- 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.
- Running
conda install --override-channels -c conda-forge -c bioconda -c defaults samtools=1.9
to downgrade samtools.
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.
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.
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 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
.
To install IRIDA to your local Maven repository please do the following:
- Clone the IRIDA project
git clone https://github.com/phac-nml/irida.git
cd irida
- Checkout appropriate version of IRIDA
git checkout 19.01.3
- Install IRIDA to local repository
mvn clean install -DskipTests
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.
The following dependencies are required in order to make use of this plugin.