Purdue University

Commands

• panaroo
• panaroo-extract-gene
• panaroo-filter-pa
• panaroo-fmg
• panaroo-gene-neighbourhood
• panaroo-img
• panaroo-integrate
• panaroo-merge
• panaroo-msa
• panaroo-plot-abundance
• panaroo-qc
• panaroo-spydrpick

Module

You can load the modules by:

module load biocontainers
module load panaroo

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 panaroo on our clusters:

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

module --force purge
ml biocontainers panaroo

panaroo -i gff/*.gff -o results --clean-mode strict