ncbi-datasets
Link to section 'Introduction' of '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.
Docker hub: https://hub.docker.com/r/staphb/ncbi-datasets
Home page: https://github.com/ncbi/datasets
Link to section 'Versions' of 'ncbi-datasets' Versions
- 14.3.0
Link to section 'Commands' of 'ncbi-datasets' Commands
- datasets
- dataformat
Link to section 'Module' of 'ncbi-datasets' Module
You can load the modules by:
module load biocontainers
module load ncbi-datasets
Link to section 'Example job' of 'ncbi-datasets' 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-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