Installation
-
Clone this directory and ShortBRED into a local folder:
git clone https://github.com/eclarke/shortbred-snakemake my_project cd my_project hg clone https://bitbucket.org/biobakery/shortbred
-
Download the marker genes for CARD from the ShortBRED website:
wget https://bitbucket.org/biobakery/shortbred/downloads/ShortBRED_CARD_2017_markers.faa.gz gunzip ShortBRED_CARD_2017_markers.faa.gz
-
Get a copy of USEARCH for Linux and install it somewhere. Update the path in the Snakefile to point to wherever you installed
usearch
. By default it looks in$HOME/bin/usearch
. -
Create a new Conda environment with Sunbeam (assumes you have Miniconda or similar installed):
conda create -n my_project -c bioconda snakemake
-
Copy or symlink your QC'd, decontaminated, paired reads to a folder in this folder (e.g.
data_files
)ln -s /some/other/project/sunbeam_output/assembly/paired data_files
Running ShortBRED
-
Activate your new Conda environment:
source activate my_project
-
Test to make sure Snakemake works correctly (in the folder we made above):
snakemake -n
. It should output a list of tasks it will perform (but not actually do it yet). -
To actually run this, use the command
snakemake --use-conda
so that it creates a new Python 2.7 environment for ShortBRED. Always use the--use-conda
flag when running these rules. -
Have fun! I ran this command on PMACS, for reference:
snakemake --use-conda --cluster "bsub -n 12" -j100