This is an extension to the Sunbeam pipeline that runs RGI (Resistance Gene Identifier) to identify antibiotic resistance genes. Check out Jia et al 2017 to learn more about RGI and CARD.
To install:
sunbeam extend https://github.com/sunbeam-labs/sbx_coassembly/
Config options for sbx_rgi are automatically added on sunbeam init. If you're installing an extension in a project where you already have a config file, run the following to add the options for your newly added extension to your config (the -i flag means in-place config file modification; remove the -i flag to see the new config in stdout):
sunbeam config update -i sunbeam_config.yml
As of December 2019, the latest CARD database version is automatically grabbed by the extension, so no need to worry about dbs!
See legacy install instructions below.
To run sbx_rgi, simply run Sunbeam as usual with the all_rgi target rule specified:
sunbeam run --configfile=sunbeam_config.yml --use-conda all_rgi
The --use-conda flag is required to let Snakemake know that you want to use the conda environment(s) included with your extension.
sbx_rgi_env.ymlspecifies the extension's dependenciesconfig.ymlcontains configuration options that can be specified by the user when running sbx_rgisbx_rgi.rulescontains the rules (logic/commands run) of the extension
Clone the extension directory into the sunbeam/extensions/ folder:
git clone https://github.com/louiejtaylor/sbx_rgi/ sunbeam/extensions/sbx_template
(Make sure you're in the correct Conda env, if not, run source activate sunbeam)
Add the new options to your existing configuration file:
cat sunbeam/extensions/sbx_rgi/config.yml >> sunbeam_config.yml