Pilon-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=pilon.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=pilon.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=pilon.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml pilon/1.22-Java-1.8.0_144 | 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 --help | |||
</pre> | </pre> | ||
Revision as of 13:05, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
1.22
Author / Distributor
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
#SBATCH --error=pilon.%j.err
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 --help
Installation
Source code is obtained from pilon
System
64-bit Linux