Purdue University

Commands

• anomaly
• build-fixed
• build-icm
• entropy-profile
• entropy-score
• extract
• g3-from-scratch.csh
• g3-from-training.csh
• g3-iterated.csh
• get-motif-counts.awk
• glim-diff.awk
• glimmer3
• long-orfs
• match-list-col.awk
• multi-extract
• not-acgt.awk
• score-fixed
• start-codon-distrib
• test
• uncovered
• upstream-coords.awk
• window-acgt

Module

You can load the modules by:

module load biocontainers
module load glimmer

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 Glimmer on our clusters:

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

module --force purge
ml biocontainers glimmer

long-orfs -n -t 1.15 scaffolds.fasta run1.longorfs
extract -t scaffolds.fasta run1.longorfs > run1.train
build-icm -r run1.icm < run1.train
glimmer3 scaffolds.fasta run1.icm cm