RevBayes-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.1.0, 1.2.1

Author / Distributor

RevBayes

Description

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

Running Program

Version 1.2.1 is installed as software module and can be loaded into your software environment with

ml RevBayes/1.2.1-gompi-2022a

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 an interactive 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