==== SRA Toolkit ====

[[https://github.com/ncbi/sra-tools/wiki|SRA Toolkit]]

=== Job SRA Toolkit ===

Example script ''slurm-sratoolkit.sh'' to run ''fastq-dump'' on 1 node of the ''cpu'' partition using 2 cores and at most 4 GB of memory:

<code bash slurm-sratoolkit.sh>
#!/bin/bash --login
#SBATCH --job-name=sratoolkit
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=4G
#SBATCH --partition=cpu
#SBATCH --qos=cpu
#SBATCH --time=0-01:00:00
##SBATCH --account=<account>

shopt -q login_shell || exit 1

module load sratoolkit

fastq-dump --stdout -X $SLURM_CPUS_PER_TASK SRR390728
</code>