Pygenomeviz

Introduction

pyGenomeViz is a genome visualization python package for comparative genomics implemented based on matplotlib.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/pygenomeviz
Home page: https://github.com/moshi4/pyGenomeViz#cli-examples

Versions

  • 0.2.2

  • 0.3.2

Commands

  • pgv-download-dataset

  • pgv-mmseqs

  • pgv-mummer

  • pgv-pmauve

  • python

  • python3

Module

You can load the modules by:

module load biocontainers
module load pygenomeviz

Example job

Warning

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 pygenomeviz on our clusters:

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

module --force purge
ml biocontainers pygenomeviz