Abricate
is a tool for mass screening of contigs for antimicrobial resistance or virulence genes.
For more information, please check its website: https://biocontainers.pro/tools/abricate and its home page on Github.
- 1.0.1
- abricate
You can load the modules by:
module load biocontainers module load abricate
Warning
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 Abricate on our clusters:
#!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 8 #SBATCH --job-name=abricate #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge ml biocontainers abricate abricate --threads 8 *.fasta