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]

optional arguments:
  -h, --help            show this help message and exit
  -f FASTA, --fasta FASTA
  -g GFF, --gff GFF
  -v, --version         show program's version number and exit
  -a ANNO, --anno ANNO
  -t TRIM, --trim TRIM
  -o OUT, --out OUT
  --fix_start_stop
  --fix_terminal_ns
  -rcs REMOVE_CDS_SHORTER_THAN, --remove_cds_shorter_than REMOVE_CDS_SHORTER_THAN
  -rcl REMOVE_CDS_LONGER_THAN, --remove_cds_longer_than REMOVE_CDS_LONGER_THAN
  -res REMOVE_EXONS_SHORTER_THAN, --remove_exons_shorter_than REMOVE_EXONS_SHORTER_THAN
  -rel REMOVE_EXONS_LONGER_THAN, --remove_exons_longer_than REMOVE_EXONS_LONGER_THAN
  -ris REMOVE_INTRONS_SHORTER_THAN, --remove_introns_shorter_than REMOVE_INTRONS_SHORTER_THAN
  -ril REMOVE_INTRONS_LONGER_THAN, --remove_introns_longer_than REMOVE_INTRONS_LONGER_THAN
  -rgs REMOVE_GENES_SHORTER_THAN, --remove_genes_shorter_than REMOVE_GENES_SHORTER_THAN
  -rgl REMOVE_GENES_LONGER_THAN, --remove_genes_longer_than REMOVE_GENES_LONGER_THAN
  -fcs FLAG_CDS_SHORTER_THAN, --flag_cds_shorter_than FLAG_CDS_SHORTER_THAN
  -fcl FLAG_CDS_LONGER_THAN, --flag_cds_longer_than FLAG_CDS_LONGER_THAN
  -fes FLAG_EXONS_SHORTER_THAN, --flag_exons_shorter_than FLAG_EXONS_SHORTER_THAN
  -fel FLAG_EXONS_LONGER_THAN, --flag_exons_longer_than FLAG_EXONS_LONGER_THAN
  -fis FLAG_INTRONS_SHORTER_THAN, --flag_introns_shorter_than FLAG_INTRONS_SHORTER_THAN
  -fil FLAG_INTRONS_LONGER_THAN, --flag_introns_longer_than FLAG_INTRONS_LONGER_THAN
  -fgs FLAG_GENES_SHORTER_THAN, --flag_genes_shorter_than FLAG_GENES_SHORTER_THAN
  -fgl FLAG_GENES_LONGER_THAN, --flag_genes_longer_than FLAG_GENES_LONGER_THAN
  -ses, --skip_empty_scaffolds

    Docs at http://genomeannotation.github.io/GAG/
    Bugs and feature requests at https://github.com/genomeannotation/GAG/issues

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Installation

Source code is obtained from GAG

System

64-bit Linux