RevBayes-Teaching - Revision history

Shtsai at 01:30, 5 April 2026

2026-04-05T01:30:36Z

← Older revision		Revision as of 21:30, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==
	1.2.5		1.2.5

	=== Author / Distributor ===		== Author / Distributor ==

	[https://github.com/revbayes/revbayes RevBayes]		[https://github.com/revbayes/revbayes RevBayes]

	=== Description ===		== Description ==
	"		"
	Bayesian phylogenetic inference using probabilistic graphical models and an interactive language."		Bayesian phylogenetic inference using probabilistic graphical models and an interactive language."
	More details are at [https://github.com/revbayes/revbayes RevBayes]		More details are at [https://github.com/revbayes/revbayes RevBayes]

	=== Running Program ===		== Running Program ==

	Version 1.2.5 is installed as software module and can be loaded into your software environment with		Version 1.2.5 is installed as software module and can be loaded into your software environment with
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	</pre>		</pre>
	-->		-->
	=== Documentation ===		== Documentation ==

	Please see http://revbayes.github.io		Please see http://revbayes.github.io
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Singularity image obtained from [https://github.com/revbayes/revbayes/releases RevBayes]		Singularity image obtained from [https://github.com/revbayes/revbayes/releases RevBayes]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 20:43, 9 January 2026

2026-01-09T20:43:55Z

← Older revision		Revision as of 16:43, 9 January 2026
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	=== Version ===		=== Version ===
	~~1.1.0,~~ 1.2.1		1.2.5

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	Version 1.2.1 is installed as software module and can be loaded into your software environment with		Version 1.2.5 is installed as software module and can be loaded into your software environment with

	<pre class="gcommand">		<pre class="gcommand">
	ml RevBayes/1.2.1-gompi-~~2022a~~		ml RevBayes/1.2.5-gompi-2023a
	</pre>		</pre>

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

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	</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.
			-->
	Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.		Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application \| Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] for more details of running jobs at Teaching cluster.

			<!--
	Here is an example of job submission command:		Here is an example of job submission command:
	<pre class="gcommand">		<pre class="gcommand">
	sbatch ./sub.sh		sbatch ./sub.sh
	</pre>		</pre>
			-->
	=== Documentation ===		=== Documentation ===

Chelsea: /* Version */

2024-05-14T12:46:03Z

Version

← Older revision		Revision as of 08:46, 14 May 2024
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	=== Version ===		=== Version ===
	1.1.0		1.1.0, 1.2.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== 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		Version 1.1.0 of this application is installed as a singularity image: /apps/singularity-images/RevBayes_1.1.0.simg
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	No module needs to be loaded to use this version of RevBayes.		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		If you would like to use it with an interactive shell, please first start an interactive session and then run

	<pre class="gcommand">		<pre class="gcommand">

Shtsai: /* Documentation */

2021-01-27T21:16:21Z

Documentation

← Older revision		Revision as of 17:16, 27 January 2021
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	Please see http://revbayes.github.io		Please see http://revbayes.github.io
	~~</pre>~~
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Shtsai: /* Running Program */

2021-01-27T21:15:32Z

Running Program

← Older revision		Revision as of 17:15, 27 January 2021
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	<pre class="gcommand">		<pre class="gcommand">
	singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg		singularity run --app rb /apps/singularity-images/RevBayes_1.1.0.simg
	<\pre>		</pre>

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

Shtsai at 21:14, 27 January 2021

2021-01-27T21:14:29Z

← Older revision		Revision as of 17:14, 27 January 2021
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	=== Version ===		=== Version ===
	1.0~~.10~~		1.1.0

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	~~The last version~~ of this application is ~~at /usr/local~~/apps/~~gb/RevBayes~~/1.0.10		Version 1.1.0 of this application is installed as a singularity image: /apps/singularity-images/RevBayes_1.1.0.simg

	To use this version, please ~~load~~ the ~~module with~~		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">
	~~ml RevBayes~~/1.0.10		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>
	~~ml RevBayes~~/1.0.~~10<br>~~
	rb <u>~~[options]~~</u><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 ===

	~~<pre~~ ~~class="gcommand">~~		Please see http://revbayes.github.io
	~~ml RevBayes/1.0.10~~
	~~rb -h~~
	~~Usage: rb [OPTIONS]~~
	~~rb [OPTIONS] <file1> [<file2> ...]~~
	~~Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language~~

	~~Options:~~
	~~-h [ --help ] Show information on flags.~~
	~~-v [ --version ] Show version and exit.~~
	~~-b [ --batch ] Run in batch mode.~~
	~~--file arg File(s) to source.~~
	~~--setOption arg Set an option key=value.~~

	~~See~~ http://revbayes.github.io ~~for more information~~
	</pre>		</pre>
	[[#top\|Back to Top]]		[[#top\|Back to Top]]
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	=== Installation ===		=== Installation ===

	~~Source code is~~ obtained from [https://github.com/revbayes/revbayes/releases RevBayes]		Singularity image obtained from [https://github.com/revbayes/revbayes/releases RevBayes]

	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Yhuang: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.0.10 ===..."

2019-01-09T16:17:46Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 1.0.10 ===..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
1.0.10

=== Author / Distributor ===

[https://github.com/revbayes/revbayes RevBayes]

=== Description ===
"
Bayesian phylogenetic inference using probabilistic graphical models and an interactive language."
More details are at [https://github.com/revbayes/revbayes RevBayes]

=== Running Program ===

The last version of this application is at /usr/local/apps/gb/RevBayes/1.0.10

To use this version, please load the module with
<pre class="gscript">
ml RevBayes/1.0.10
</pre>

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

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_RevBayes 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=RevBayes.%j.out 
<nowiki>#</nowiki>SBATCH --error=RevBayes.%j.err 

cd $SLURM_SUBMIT_DIR 
ml RevBayes/1.0.10 
rb [options] 
</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.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
ml RevBayes/1.0.10
rb -h
Usage: rb [OPTIONS]
rb [OPTIONS] <file1> [<file2> ...]
Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language

Options:
-h [ --help ] Show information on flags.
-v [ --version ] Show version and exit.
-b [ --batch ] Run in batch mode.
--file arg File(s) to source.
--setOption arg Set an option key=value.

See http://revbayes.github.io for more information
</pre>
[[#top|Back to Top]]

=== Installation ===

Source code is obtained from [https://github.com/revbayes/revbayes/releases RevBayes]

=== System ===
64-bit Linux