rampart-nipah

RAMPART protocol folder for Nipah and Hendra viruses

Installing

Clone this repository:

git clone https://github.com/artic-network/rampart-nipah.git

Create conda environment and activate it:

cd rampart-artic
conda env create -f environment.yml
conda activate rampart-artic

Running

Create run folder:

mkdir [run_name]
cd [run_name]

Where [run_name] is whatever you are calling todays run (as specified in MinKNOW).

Run RAMPART (assuming the rampart-nipah directory is next to [run_name]):

rampart --protocol ../rampart-nipah/protocol --basecalledPath ~/MinKNOW/data/reads/[run_name]/pass

basecalledPath should be set to whereever MinKNOW/guppy is going to write its basecalled files.

Example Data

The directory example_data contains some reads from a Nipah virus MinION run to test RAMPART with. To try this:

cd rampart/example_data
rampart --protocol ../protocol 

The run_configuration.json file contains the settings for running this example data.

Open a browser to view http://localhost:3000