GAG-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.0.1

Author / Distributor

GAG

Description

"GAG - Genome Annotation Generator: Command line application to read, sanitize, annotate and modify genomic data." More details are at GAG

Running Program

The last version of this application is at /usr/local/apps/eb/GAG/2.0.1-foss-2016b

To use this version, please load the module with

ml GAG/2.0.1-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_GAG
#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=GAG.%j.out
#SBATCH --error=GAG.%j.err

cd $SLURM_SUBMIT_DIR
ml GAG/2.0.1-foss-2016b
python /usr/local/apps/eb/GAG/2.0.1-foss-2016b/gag.py [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

ml GAG/2.0.1-foss-2016b 
python /usr/local/apps/eb/GAG/2.0.1-foss-2016b/gag.py -h

Back to Top

Installation

Source code is obtained from GAG

System

64-bit Linux