RAMPART protocol folder for Nipah and Hendra viruses
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
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.
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