With your sunbeam conda environment activated,
-
Clone into your Sunbeam directory:
git clone https://github.com/sunbeam-labs/sbx_kaiju sunbeam/extensions/sbx_kaiju
-
Install the requirements:
conda install --file sunbeam/extensions/sbx_kaiju/requirements.txt
-
Add the new config options to your config file:
cat sunbeam/extensions/sbx_kaiju/config.yml >> my_config.yml
This adds a new rule, all_kaiju
. Specify this as your target to use Kaiju to classify your decontaminated samples.