Purdue University

Commands

• make_fasta_from_fastg.py
• get_simple_cycs.py
• recycle.py

Module

You can load the modules by:

module load biocontainers
module load recycler

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 Recycler on our clusters:

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

module --force purge
ml biocontainers recycler

recycle.py -g test/assembly_graph.fastg \ 
    -k 55 -b test/test.sort.bam -i True