MSG-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.4.9

Author / Distributor

Please see https://github.com/JaneliaSciComp/msg

Description

The MSG application is a Multiplexed Shotgun Genotyping suite of programs. For more information, please see https://github.com/JaneliaSciComp/msg and http://genomics.princeton.edu/AndolfattoLab/MSG.html

Running Program

Also refer to Running Jobs on the teaching cluster

For more information on Environment Modules on Sapelo2 please see the Lmod page.

• Version 0.4.9, installed in /usr/local/apps/eb/MSG/0.4.9-foss-2016b-Python-2.7.14

To use this version of MSG, please first load the module with

ml MSG/0.4.9-foss-2016b-Python-2.7.14

This module automatically loads Python/2.7.14-foss-2016b, Biopython/1.68-foss-2016b-Python-2.7.14, Perl/5.24.1-foss-2016b, R/3.4.4-foss-2016b-X11-20160819-GACRC, BWA/0.5.7-foss-2016b, SAMtools/0.1.9-foss-2016b, Pyrex/0.9.9-foss-2016b-Python-2.7.14, Pysam/0.1.2-foss-2016b-Python-2.7.14, and other dependencies.

Sample job submission script (sub.sh) to run msg.pl:

#!/bin/bash
#SBATCH --job-name=j_MSG
#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=MSG.%j.out
#SBATCH --error=MSG.%j.err

cd $SLURM_SUBMIT_DIR
ml MSG/0.4.9-foss-2016b-Python-2.7.14
msg.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.

Submit the job to the queue with

sbatch sub.sh

Documentation

Please see http://genomics.princeton.edu/AndolfattoLab/MSG.html and https://github.com/JaneliaSciComp/msg

Installation

• Version 0.4.9, source code downloaded with

git clone git://github.com/JaneliaSciComp/msg.git

System

64-bit Linux