Initial release of amr detection pipeline

[apetkau]

This implements the initial release of the AMR detection pipeline (implementing issue https://github.com/phac-nml/irida/issues/137).

In order to test this out you have to first start up a Galaxy instance and install the following tools:

• RGI https://toolshed.g2.bx.psu.edu/view/card/rgi/715bc9aeef69
• staramr https://toolshed.g2.bx.psu.edu/view/nml/staramr/930893c83a1a
• shovill https://toolshed.g2.bx.psu.edu/view/iuc/shovill/865119fcb694

Once you've got those tools installed, you will have to build the plugin. This first requires you to install IRIDA to your Maven repository:

# Run this in the irida project
cd irida

# Checkout specific version I compile against
git checkout 19.01.3
mvn clean install -DskipTests

Now, to build you can run:

# Run this in this code repository
cd irida-plugin-amr-detection

mvn clean package

Now, to install the plugin, you can run:

cp target/*.java /etc/irida/plugins

Now, start up IRIDA and you can run the AMR Detection pipeline.