Difference between revisions of "BEAST"

From UFRC
Jump to navigation Jump to search
Line 53: Line 53:
  
 
==Interactive beauti use==
 
==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:
+
To connect to a test node, for example test05, 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:
  ssh USER@biotest.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@submit.hpc.ufl.edu exec nc test05 %p'
+
  ssh USER@test05.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@submit.hpc.ufl.edu exec nc test05 %p'
 
or add the following to your ~/.ssh/config file:
 
or add the following to your ~/.ssh/config file:
  Host biotest
+
  Host test05
 
     User USER
 
     User USER
 
     KeepAlive yes
 
     KeepAlive yes
Line 64: Line 64:
  
 
where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:
 
where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:
  ssh biotest
+
  ssh test05
  
 
Once connected run
 
Once connected run

Revision as of 21:40, 13 July 2012

Description

{{{name}}} website  
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. Template:App Location

Available versions

  • 1.6.2
  • 1.7.0
  • 1.7.1 (default)

Running the application using modules

To use beast with the environment modules system at HPC the following commands are available:

Get module information for beast:

$module spider beast

Load the default application module:

$module load beast

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_BEAST_DIR - directory where beast is located.
  • HPC_BEAST_BIN - executable directory
  • HPC_BEAST_DOC - docs directory
  • BEAST - Beast directory

For example:

export _JAVA_OPTIONS="-Xms1024m -Xmx2048m"

Galaxy

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

Interactive beauti use

To connect to a test node, for example test05, 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:

ssh USER@test05.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@submit.hpc.ufl.edu exec nc test05 %p'

or add the following to your ~/.ssh/config file:

Host test05
   User USER
   KeepAlive yes
   ProxyCommand ssh USER@submit.hpc.ufl.edu exec nc test05 %p
   ForwardX11 yes
   ForwardX11Trusted yes

where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:

ssh test05

Once connected run

module load beast
beauti