Pbptyper

Introduction

pbptyper is a tool to identify the Penicillin Binding Protein (PBP) of Streptococcus pneumoniae assemblies.

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/pbptyper

Home page: https://github.com/rpetit3/pbptyper

Versions

• 1.0.4

Commands

• pbptyper

Module

You can load the modules by:

module load biocontainers
module load pbptyper

Example job

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 pbptyper on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pbptyper
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pbptyper

pbptyper --assembly test/SRR2912551.fna.gz --outdir output