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.   
Line 60: Line 60:
<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
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
 


</pre>
</pre>

Revision as of 11:20, 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

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