Pilon-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.22

Author / Distributor

pilon

Description

"Pilon is a software tool which can be used to: (i) Automatically improve draft assemblies, (ii)Find variation among strains, including large event detection" More details are at pilon

Running Program

The last version of this application is at /usr/local/apps/eb/pilon/1.22-Java-1.8.0_144

To use this version, please load the module with

ml pilon/1.22-Java-1.8.0_144 

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

#!/bin/bash
#SBATCH --job-name=j_pilon
#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=pilon.%j.out

cd $SLURM_SUBMIT_DIR
ml pilon/1.22-Java-1.8.0_144
java-jar/usr/local/apps/eb/pilon/1.22-Java-1.8.0_144/pilon-1.22.jar [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 pilon/1.22-Java-1.8.0_144 
java-jar/usr/local/apps/eb/pilon/1.22-Java-1.8.0_144/pilon-1.22.jar java-jar/usr/local/apps/eb/pilon/1.22-Java-1.8.0_144/pilon-1.22.jar --help

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Installation

Source code is obtained from pilon

System

64-bit Linux