Helen

Introduction

HELEN is a multi-task RNN polisher which operates on images produced by MarginPolish.

For more information, please check:

Docker hub: https://hub.docker.com/r/kishwars/helen

Home page: https://github.com/kishwarshafin/helen

Versions

• 1.0

Commands

• helen

Module

You can load the modules by:

module load biocontainers
module load helen

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 helen on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 32
#SBATCH --job-name=helen
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers helen

helen polish \
    --image_dir mp_output \
    --model_path "helen_modles/HELEN_r941_guppy344_microbial.pkl" \
    --threads 32 \
    --output_dir "helen_output/" \
    --output_prefix Staph_Aur_draft_helen