RevBayes-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.1.0

Author / Distributor

RevBayes

Description

" Bayesian phylogenetic inference using probabilistic graphical models and an interactive language." More details are at RevBayes

Running Program

Version 1.1.0 of this application is installed as a singularity image: /apps/singularity-images/RevBayes_1.1.0.simg

No module needs to be loaded to use this version of RevBayes.

If you would like to use it with an interactive shell, please first start a qlogin session and then run

singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg

You can run a script in a batch job by using the following line in your job submission script:

singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg myscript.rev

where myscript.rev is a sample name for a RevBayes script.

Here is an example of a shell script, sub.sh, to run on the batch queue:

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

cd $SLURM_SUBMIT_DIR

singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg myscript.rev

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

Please see http://revbayes.github.io

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Installation

Singularity image obtained from RevBayes

System

64-bit Linux