examples.md

Running the provided examples

This article presupposes that you have installed RAMPART by cloning the GitHub repository.

We've provided an example to both test out RAMPART and to see how a set of working configuration files look. Start by navigating into the example directory:

cd rampart/example_data/20181008_1405_EBOV

Here you'll see a folder (./fastq/pass) with a few fastq files, basecalled by MinKNOW during an Ebola validation run. There's also a run_configuration.json file which defines some of the parameters for this run, such as the barcode-sample name mapping. The rampart GitHub repo also includes an example protocol for Ebola virus (EBOV) at rampart/example_protocols/EBOV, which we'll feed into RAMPART for this example.

Please refer to setting up for your own run for how to create these files & protocols yourself.

We can run this example for ourselves via:

rampart --protocol ../../example_protocols/EBOV --clearAnnotated

The --clearAnnotated flag will remove any results in case we've already run this example.

By opening a browser at localhost:3000 we can see the data being processed & interact with the results. It should look something like this: