BEAST

Description
	This description comes from the BEAST home page. "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."
Site	Version (Latest: v1.5.3)	Notes
ngs.oerc.ox.ac.uk	v1.5.3	Runs on Java

License

The following license conditions were copied from the BEAST website in January 2010. You should refer to the BEAST home page for up to date information. "The complete source code for BEAST is now distributed under the GNU Lesser General Public License." See the GNU General Lesser Public License.

When publishing your work using MrBayes on the NGS, you should both credit the NGS and refer to the citation suggestions on the BEAST home page. You should also credit the NGS site where you ran the code.

Running BEAST on the NGS

The example input files for all the following submission examples, benchmark.xml, can be foung at gsiftp://ngs.oerc.ox.ac.uk:2811/usr/local/Cluster-Apps/BEASTv1.5.3/examples/benchmark.xml

• Submission Using the UI/WMS

  To submit an BEAST job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a beast.jdl

  Type = "Job";
  JobType = "normal";
  Executable = "/usr/ngs/BEAST";
  Arguments = "benchmark.xml";
  StdOutput = "benchmark.out";
  StdError = "benchmark.err";
  Myproxyserver= "myproxy.ngs.ac.uk";
  InputSandbox = {"benchmark.xml"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsXXXX/beast";
  OutputSandbox = {"benchmark.out", "benchmark.err", "benchmark.log", "benchmark.trees", "mcmc.operators"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsXXXX/beast";
  Requirements = (
       member("NGS-UEE-BEAST", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  ShallowRetryCount = -1;

• Submission Using the UI/WMS

  Please contact the helpdesk if you would like to run this application via the NGS web portal

• Submission Using Globus

  BEAST is launched on the NGS using the following command:

  globusrun -b -r ngs.oerc.ox.ac.uk/jobmanager-pbs \ '&(executable=/usr/ngs/BEAST) \ (arguments= benchmark.xml)(jobType=single) \ (directory=/home/ngsXXXX/beast) \ (stdout=benchmark.out)(stderr=benchmark.err)'

  • This runs the default version.
  • stdout and stderr are set to 'benchmark.out' and 'benchmark.err' respectively.
  • The first argument is the program we want to run. (benchmark.xml in this case)
  • The input files must be given as an argument and not as stdin.
  • Replace 'ngsXXXX' by your user id on the system running the job (ngs.oerc.ox.ac.uk in this case). 'directory' is the working directory for the job, in this case a subdirectory of your homedir called 'beast'.

  Further Information

  • BEAST Home page
  • Online tutorials
  • V1.4 Manual (older version)
  • V1.5.x XML file reference
  • beast-users mailing list.