Software: ARIBA
Description
ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.
Available Versions
Unspecified: | 2.14.6 |
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Docker hub: https://hub.docker.com/r/staphb/ariba
Home page: https://github.com/sanger-pathogens/ariba
Commands
- ariba
Module
You can load the modules by:
module load biocontainers
module load ariba
Example job
Using
#!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bash
instead.
To run ariba on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ariba
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ariba