Purdue University

Commands

• ncbi-genome-download

Module

You can load the modules by:

module load biocontainers
module load ncbi-genome-download

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 Ncbi-genome-download on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=ncbi-genome-download
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers ncbi-genome-download

ncbi-genome-download bacteria,viral --parallel 4
ncbi-genome-download --genera "Streptomyces coelicolor,Escherichia coli" bacteria
ncbi-genome-download --species-taxids 562 bacteria