sbx_shortbred

Sunbeam extension for running ShortBRED.

Installation

1. Clone into your Sunbeam extensions directory and update your config file

   git clone https://github.com/sunbeam-labs/sbx_shortbred extensions/sbx_shortbred
   cat sunbeam/extensions/sbx_shortbred/config.yml >> sunbeam_config.yml
   

2. Get a copy of USEARCH and install it in your sbx_shortbred folder. Create a symlink to $CONDA_PREFIX/bin

   PWD=`pwd`
   ln -sf $PWD/usearch10.0.240_i86linux32 $CONDA_PREFIX/bin/usearch

3. Download the AR-specific marker genes for CARD from the ShortBREAD website OR use the marker genes for a newer version of CARD.

   wget https://bitbucket.org/biobakery/shortbred/downloads/ShortBRED_CARD_2017_markers.faa.gz
   gunzip ShortBRED_CARD_2017_markers.faa.gz

4. Link the marker database to the Sunbeam environment

   mkdir -p $CONDA_PREFIX/opt/shortbred_databases
   ln -sf $PWD/SHORTBRED_CARD_20180628_markers.faa $CONDA_PREFIX/opt/shortbred_databases

5. Update the Sunbeam environment.

   conda env update --name=sunbeam --quiet --file extensions/sbx_shortbred/requirements.txt

Running

This extension uses an isolated Conda environment for the ShortBRED installation, so you need to include the --use-conda argument when running Sunbeam:

sunbeam run --configfile=sunbeam_config.yml --use-conda all_card