Picard-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.16.0

Author / Distributor

picard

Description

"A set of tools (in Java) for working with next generation sequencing data in the BAM format." More details are at picard

Running Program

The last version of this application is at /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144

To use this version, please load the module with

ml picard/2.16.0-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_picard
#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=picard.%j.out
#SBATCH --error=picard.%j.err

cd $SLURM_SUBMIT_DIR
ml picard/2.16.0-Java-1.8.0_144
java-jar/usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.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 picard/2.16.0-Java-1.8.0_144 
java-jar/usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.jar -h

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Installation

Source code is obtained from picard

System

64-bit Linux