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 13:03, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
4.33
Author / Distributor
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]
Installation
Source code is obtained from GeneMarkES
System
64-bit Linux