RevBayes-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1.0. | 1.1.0, 1.2.1 | ||
=== Author / Distributor === | === Author / Distributor === | ||
| Line 22: | Line 22: | ||
=== Running Program === | === Running Program === | ||
Version 1.2.1 is installed as software module and can be loaded into your software environment with | |||
<pre class="gcommand"> | |||
ml RevBayes/1.2.1-gompi-2022a | |||
</pre> | |||
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 | |||
<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: | ||
| Line 44: | Line 59: | ||
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 | |||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
=== Installation === | === Installation === | ||
Singularity image obtained from [https://github.com/revbayes/revbayes/releases RevBayes] | |||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 08:46, 14 May 2024
Category
Bioinformatics
Program On
Teaching
Version
1.1.0, 1.2.1
Author / Distributor
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
Installation
Singularity image obtained from RevBayes
System
64-bit Linux