GeneMarkES-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=GeneMarkES.%j.out<br>
<nowiki>#</nowiki>SBATCH --output=GeneMarkES.%j.out<br>
<nowiki>#</nowiki>SBATCH --error=GeneMarkES.%j.err<br>
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>

Revision as of 14:03, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

4.33

Author / Distributor

GeneMarkES

Description

" Gene Prediction in Eukaryotes. Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training." More details are at GeneMarkES

Running Program

The last version of this application is at /usr/local/apps/gb/genemarkes/4.33

To use this version, please load the module with

ml genemarkes/4.33 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_GeneMarkES
#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=GeneMarkES.%j.out
#SBATCH --error=GeneMarkES.%j.err

cd $SLURM_SUBMIT_DIR
ml genemarkes/4.33
perl /usr/local/apps/gb/genemarkes/4.33/gmes_petap.pl [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 genemarkes/4.33 
perl /usr/local/apps/gb/genemarkes/4.33/gmes_petap.pl 
[http://exon.gatech.edu/GeneMark/ GeneMarkES]

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Installation

Source code is obtained from GeneMarkES

System

64-bit Linux