Ncbi-datasets

Introduction

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. You can use it to find and download sequence, annotation, and metadata for genes and genomes using our command-line interface (CLI) tools or NCBI Datasets web interface.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/ncbi-datasets
Home page: https://github.com/ncbi/datasets

Versions

  • 14.3.0

Commands

  • datasets

  • dataformat

Module

You can load the modules by:

module load biocontainers
module load ncbi-datasets

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 ncbi-datasets on our clusters:

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

module --force purge
ml biocontainers ncbi-datasets