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
usage: gag.py [-h] -f FASTA -g GFF [-v] [-a ANNO] [-t TRIM] [-o OUT]
              [--fix_start_stop] [--fix_terminal_ns]
              [-rcs REMOVE_CDS_SHORTER_THAN] [-rcl REMOVE_CDS_LONGER_THAN]
              [-res REMOVE_EXONS_SHORTER_THAN] [-rel REMOVE_EXONS_LONGER_THAN]
              [-ris REMOVE_INTRONS_SHORTER_THAN]
              [-ril REMOVE_INTRONS_LONGER_THAN]
              [-rgs REMOVE_GENES_SHORTER_THAN] [-rgl REMOVE_GENES_LONGER_THAN]
              [-fcs FLAG_CDS_SHORTER_THAN] [-fcl FLAG_CDS_LONGER_THAN]
              [-fes FLAG_EXONS_SHORTER_THAN] [-fel FLAG_EXONS_LONGER_THAN]
              [-fis FLAG_INTRONS_SHORTER_THAN] [-fil FLAG_INTRONS_LONGER_THAN]
              [-fgs FLAG_GENES_SHORTER_THAN] [-fgl FLAG_GENES_LONGER_THAN]
              [-ses]
gag.py: error: argument -f/--fasta is required

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Installation

Source code is obtained from GAG

System

64-bit Linux