sunbeam-labs / sbx_kaiju

Kaiju metagenomics classifier for Sunbeam

Kaiju metagenomics classifier for Sunbeam

Installation:

With your sunbeam conda environment activated,

1. Clone into your Sunbeam directory:

   git clone https://github.com/sunbeam-labs/sbx_kaiju sunbeam/extensions/sbx_kaiju

2. Install the requirements:

   conda install --file sunbeam/extensions/sbx_kaiju/requirements.txt

3. Add the new config options to your config file:

   cat sunbeam/extensions/sbx_kaiju/config.yml >> my_config.yml

Setting up databases

For help building Kaiju databases, see the Kaiju github repo. To build a database with RefSeq bacteria, viruses, and archea, use the following command:

```shell
makeDB.sh -r -p
```

Make sure to edit your config file to set the nodes_fp, names_fp, and db_fp for your shiny new database!

Usage

This adds a new rule, all_kaiju. Specify this as your target to use Kaiju to classify your decontaminated samples.

You specify it like this:

sunbeam run --configfile ~/path/to/sunbeam_config.yml --use-conda all_kaiju