pggb.rst

Pggb

Introduction ~~~~~~~~ pggb builds pangenome variation graphs from a set of input sequences.

For more information, please check:
Docker hub: https://hub.docker.com/r/pangenome/pggb
Home page: https://github.com/pangenome/pggb

Versions

• 0.5.4

Commands ~~~~~~~ - pggb

Module

You can load the modules by:

module load biocontainers
module load pggb

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 pggb on our clusters:

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

module --force purge
ml biocontainers pggb