GAG-Teaching: Difference between revisions

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cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml GAG/2.0.1-foss-2016b<br>     
ml GAG/2.0.1-foss-2016b<br>     
python/usr/local/apps/eb/GAG/2.0.1-foss-2016b/gag.py <u>[options]</u><br>   
python /usr/local/apps/eb/GAG/2.0.1-foss-2016b/gag.py <u>[options]</u><br>   
</div>
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.   
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.   
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<pre  class="gcommand">
<pre  class="gcommand">
ml GAG/2.0.1-foss-2016b  
ml GAG/2.0.1-foss-2016b  
python/usr/local/apps/eb/GAG/2.0.1-foss-2016b/gag.py =h
python /usr/local/apps/eb/GAG/2.0.1-foss-2016b/gag.py -h


</pre>
</pre>

Revision as of 14:33, 15 August 2018

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

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Installation

Source code is obtained from GAG

System

64-bit Linux