https://github.com/Gaius-Augustus/Augustus

• Module Name: augustus (see the modules page for more information)
• Example files are under /usr/local/apps/augustus/version/example*

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive --mem=10g
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ cd /data/$USER/

[cn0135]$ module load augustus

[cn0135]$ cp -rp /usr/local/apps/augustus/version/examples/example.fa /data/$USER
[cn0135]$ augustus --species=human example.fa


[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.

1. Create a script file (myscript) similar to the one below

#! /bin/bash
# myscript
set -e

module load augustus || exit 1
cd /data/$USER/
augustus --species=human example.fa

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=5g myscript

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile).

cd /data/$USER/dir1; augustus species=human example.fa
cd /data/$USER/dir2; augustus species=human example.fa
cd /data/$USER/dir3; augustus species=human example.fa
...
cd /data/$USER/dir20; augustus species=human example.fa

submit the swarm job:

$ swarm -f cmdfile --module augustus -g 5

For more information regarding running swarm, see swarm.html