helen
Link to section 'Introduction' of 'helen' Introduction
HELEN is a multi-task RNN polisher which operates on images produced by MarginPolish.
Docker hub: https://hub.docker.com/r/kishwars/helen
Home page: https://github.com/kishwarshafin/helen
Link to section 'Versions' of 'helen' Versions
- 1.0
Link to section 'Commands' of 'helen' Commands
- helen
Link to section 'Module' of 'helen' Module
You can load the modules by:
module load biocontainers
module load helen
Link to section 'Example job' of 'helen' 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 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