Difference between revisions of "BEAST"

Revision as of 18:14, 12 August 2022

Description

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Environment Modules

Run module spider beast to find out what environment modules are available for this application.

System Variables

HPC_BEAST_DIR - installation directory

Galaxy

Beast is also available for use through the friendly web interface of the UFRC Galaxy instance. It's located in the "Phylogenetics" section.

Interactive beauti use

In short, you have to use a SLURM GUI session and specify the module you want as the default beast module could be different from the one you'd like to run.

E.g.

module load gui
gui start --module beast/2.6.0 -e beauti

See GUI Programs for reference.

Some versions of BEAST/BEAUTI may be available in OnDemand.

Additional Information

Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a GPU Job
To use CPU acceleration the beagle library use the '-beagle_SSE -beagle_instances N' command line switches where 'N' equals to the number of requested Beagle library instances.
To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the '-threads N' where 'N' is the number of threads. Then, the job resource request should be equal to nodes=1:ppn=X where X = N + 1.
General performance considerations - http://www.beast2.org/beagle-beast-2-in-cluster/.
Beast2 plugins are installed into your personal directory. This means that you need to start Beauti and install plugins manually.

@@ Line 1: / Line 1: @@
 __NOTOC__
 __NOEDITSECTION__
-[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
+[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|beast}}
-|{{#vardefine:url|http://beast.bio.ed.ac.uk/Main_Page}}
+|{{#vardefine:url|http://www.beast2.org}}
-<!--Compiler and MPI settings - OPTIONAL -->
+|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
-|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
-|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
-|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
@@ Line 31: / Line 16: @@
 <!--Description-->
 {{#if: {{#var: url}}|
-{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
+{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
-<!--Location-->
+<!--Modules-->
-{{App_Location|app={{#var:app}}|{{#var:ver}}}}
+==Environment Modules==
-==Available versions==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* 1.6.2
+==System Variables==
-* 1.7.0
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* 1.7.1 (default)
-<!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
-* HPC_BEAST_BIN - executable directory
-* HPC_BEAST_LIB - library directory
-* HPC_BEAST_DOC - docs directory
 ==Galaxy==
-Beast is also available for use through the friendly web interface of the [http://galaxy.hpc.ufl.edu/root?tool_id=beast UF HPC Galaxy instance]. It's located in the "Phylogenetics" section.
+Beast is also available for use through the friendly web interface of the [http://galaxy.rc.ufl.edu/root?tool_id=beast UFRC Galaxy instance]. It's located in the "Phylogenetics" section.
 ==Interactive beauti use==
-To connect to a test node, for example biotest, where you can run the graphical beauti software to build an xml file for the BEAST use the following or a similar command on a linux or MacOS X system:
+In short, you have to use a [[GUI Programs|SLURM GUI]] session and specify the module you want as the default beast module could be different from the one you'd like to run.
- ssh USER@biotest.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@bio.hpc.ufl.edu exec nc biotest %p'
-or add the following to your ~/.ssh/config file:
+E.g.
-  Host biotest
+ module load gui
-    User USER
+  gui start --module beast/2.6.0 -e beauti
-    KeepAlive yes
-    ProxyCommand ssh USER@bio.hpc.ufl.edu exec nc biotest %p
+See [[GUI Programs]] for reference.
-    ForwardX11 yes
-    ForwardX11Trusted yes
-where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:
+Some versions of BEAST/BEAUTI may be available in [https://ood.rc.ufl.edu OnDemand].
- ssh biotest
-Once connected run
+<!--Additional-->
- module load beast
+{{#if: {{#var: exe}}|==Additional Information==
- beauti
+* Use -beagle_GPU beast command-line argument to invoke BEAST with GPU acceleration when running in a [[GPU_Access|GPU Job]]
-{{#if: {{#var: exe}}|==How To Run==
+* To use CPU acceleration the beagle library use the <code>'-beagle_SSE -beagle_instances N'</code> command line switches where 'N' equals to the number of requested Beagle library instances.
-WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
+* To limit the number of computing cores Beast will use for posterior computation to the number requested from the batch system use the <code>'-threads N'</code> where 'N' is the number of threads. Then, the job resource request should be equal to <code>nodes=1:ppn=X</code> where X = N + 1.
+* General performance considerations - [http://www.beast2.org/beagle-beast-2-in-cluster/ http://www.beast2.org/beagle-beast-2-in-cluster/].
+* Beast2 plugins are installed into your personal directory. This means that you need to start Beauti and install plugins manually.
+|}}
 {{#if: {{#var: conf}}|==Configuration==
 See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==