In this extension, we show how easy it is to add downstream analysis to sunbeam pipeline as an extension.
To install:
sunbeam extend https://github.com/sunbeam-labs/sbx_anvio
Legacy instructions for older Sunbeam versions are below.
This adds a new rule, all_anvio_scg. Specify this as your target to use Anvio to look at the distributuion of bacterial single-copy genes in this contigs database, and roughly predict the number of genomes in it:
sunbeam run --configfile sunbeam_config.yml --use-conda all_anvio_scg
The --use-conda flag is required to let Snakemake know that you want to use the sbx_anvio conda environment.
With your sunbeam conda environment activated,
- Clone into your Sunbeam directory:
git clone https://github.com/sunbeam-labs/sbx_anvio sunbeam/extensions/sbx_anvio