00Template-sapelo2

Category

Bioinformatics

Program On

Sapelo2

Running Program

Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo please see the Lmod page. T o find all versions of app installed on Sapelo2, please use module spider command to do a search, as shown below:

module spider app

Example of a shell script sub.sh to run blastn on the batch partition:

#!/bin/bash
#SBATCH --job-name=appjob
#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=%x.%j.out
#SBATCH --error=%x.%j.err
cd $SLURM_SUBMIT_DIR
ml app/version-toolchain
app [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

Submit the job to the queue with

sbatch ./sub.sh

Documentation

 
module load app/version-toolchain
appname -help

Installation

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