The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Maintenance Notice for July 23, 2019

On Tuesday, July 23, CyVerse will be performing a Ceph storage upgrade from 11:00 AM to 5:00 PM MST. This is not expected to cause disruptions to the affected services. The services to be upgraded include:
- CyVerse authentication (CAS), which provides authentication to CyVerse web applications, e.g., the Discovery Environment and User Portal
- Atmosphere
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BEAST2 on CyVerse UK

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This is BEAST version 2.4.3 on the CyVerse UK hardware (12 cpus, 256 GB per job). It is software for Bayesian analysis of molecular sequences using MCMC. See http://beast2.org for more info.

Quick Start

  • This is a fairly simple app in terms of inputs and outputs, all it needs is a BEAST batch XML file which contains a sequence alignment and all options necessary for the program. See the example file in the example data. Also see the detailed guides on this file format here: http://beast2.org/tutorials/

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> BEAST2_uk

Input File(s)

Only one file is necessary, the alignment and option xml file.

Output Files

  • beast.err, beast.log, beast.out - standard error, out and log
  • filename.log - log file of this run
  • filename.ops - cpu operations log of this run
  • filename.trees - all trees produced during the run

Other files may appear depending on your model, partitions, options etc...

Tool Source for App

https://github.com/CompEvol/beast2

 

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