Pangolin

Introduction

Pangolin is a software package for assigning SARS-CoV-2 genome sequences to global lineages.

For more information, please check its website: https://biocontainers.pro/tools/pangolin and its home page on Github.

Versions

• 3.1.20

• 4.0.6

• 4.1.2

• 4.1.3

• 4.2

Commands

• pangolin

Module

You can load the modules by:

module load biocontainers
module load pangolin

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 Pangolin on our clusters:

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

module --force purge
ml biocontainers pangolin