Purdue University

Commands

• anchorwave
• gmap_build
• gmap
• minimap2

Module

You can load the modules by:

module load biocontainers
module load anchorwave

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 Anchorwave on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=anchorwave
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers anchorwave

anchorwave gff2seq -i Zea_mays.AGPv4.34.gff3 -r Zea_mays.AGPv4.dna.toplevel.fa -o cds.fa