Ncbi-genome-download¶
Introduction¶
Ncbi-genome-download
is a script to download genomes from the NCBI FTP servers.
For more information, please check its website: https://biocontainers.pro/tools/ncbi-genome-download and its home page on Github.
Versions¶
0.3.1
Commands¶
ncbi-genome-download
Module¶
You can load the modules by:
module load biocontainers
module load ncbi-genome-download
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-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