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> | |||
</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 | |||
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 15:14, 10 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] 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
Installation
Source code is obtained from GAG
System
64-bit Linux