GAG-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=GAG.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=GAG.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=GAG.%j.err<br> | |||
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> | |||
</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 59: | 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 | |||
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 | |||
</pre> | </pre> | ||
Latest revision as of 14:22, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.0.1
Author / Distributor
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
Installation
Source code is obtained from GAG
System
64-bit Linux