Picard-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=picard.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=picard.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=picard.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml picard/2.16.0-Java-1.8.0_144 | 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 | |||
</pre> | </pre> | ||
Revision as of 14:05, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.16.0
Author / Distributor
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
Installation
Source code is obtained from picard
System
64-bit Linux