RevBayes-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1.0 | 1.1.0 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Running Program === | === 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 | |||
<pre class="gcommand"> | |||
singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg | |||
<\pre> | |||
You can run a script in a batch job by using the following line in your job submission script: | |||
<pre class="gscript"> | <pre class="gscript"> | ||
singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg myscript.rev | |||
</pre> | </pre> | ||
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: | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg <u>myscript.rev</u><br> | |||
</div> | </div> | ||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | ||
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=== Documentation === | === Documentation === | ||
Please see http://revbayes.github.io | |||
</pre> | </pre> | ||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
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=== Installation === | === Installation === | ||
Singularity image obtained from [https://github.com/revbayes/revbayes/releases RevBayes] | |||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Revision as of 17:14, 27 January 2021
Category
Bioinformatics
Program On
Teaching
Version
1.1.0
Author / Distributor
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 <\pre> You can run a script in a batch job by using the following line in your job submission script: <pre class="gscript"> 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
Installation
Singularity image obtained from RevBayes
System
64-bit Linux