rampart

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:

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