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