SRA-Toolkit
Category
Bioinformatics
Program On
Sapelo2
Version
2.9.6-1-centos_linux64, 2.10.8-centos_linux64, 2.11.1-centos_linux64,
Author / Distributor
Description
"The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives." More details are at SRA-ToolKit
Running Program
The last version of this application is at /apps/eb/SRA-Toolkit/2.11.1-centos_linux64
To use this version, please load the module with
ml SRA-Toolkit/2.11.1-centos_linux64
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_BLAST+
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BLAST+.%j.out
#SBATCH --error=BLAST+.%j.err
cd $SLURM_SUBMIT_DIR
ml ----------------
[options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
-----------------------------------
Installation
System
64-bit Linux