Software: Pangolin
Description
Pangolin is a software package for assigning SARS-CoV-2 genome sequences to global lineages.
Available Versions
| Unspecified: | 3.1.20 4.0.6 4.1.2 4.1.3 4.2.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/pangolin and its home page on Github.
Commands
- pangolin
Module
You can load the modules by:
module load biocontainers
module load pangolin
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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