Setting up Hudson 

Preliminaries: we need vncserver to be set up for Fest based tests. This involves setting up vncserver on the Hudson machine and installing the Xvnc plugin on Hudson

Setting up vncserver on Hudson machine 

install vnc4server

   sudo apt-get install vnc4server

set up password for vncserver for user hudson

1. log in as hudson (or whatever user the hudson process runs under)

   sudo su - hudson

2. start up vncserver, this asks for pwd


3. kill vncserver (assuming vncserver was started on display 1)

   vncserver -kill :1

Setting up Xvnc-plugin on Hudson 

Go to Hudson main page

Click Manage Hudson

Click Manage Plugins

Select ‘Hudson Xvnc plugin’ from available plugins and click install at bottom of page

Goto Manage Hudson, click Configure System

Under Xvnc, entere for Command line

   /usr/bin/vncserver :$DISPLAY_NUMBER -geometry 1280x1024

Enter for base display number


Click Save

Setting up Hudson for BEAST2 

Assuming Hudson is installed — as it is currently at

  1. create Hudson project BEAST2 through the web interface
  2. under Source Code Management, click Subversion, and enter

Repository URL: and Local module directory (optional) beast2

  1. under build triggers, set Poll SCM to ‘* * * * *’
  2. make sure that the Ant target is build_jar_all_BEAST
  3. under Post-build actions, check Publish Junit test result reports, and enter beast2/build/junitreport/*.xml
  4. ssh into hudson machine and go to the directory /usr/share/tomcat6/.hudson/jobs
  5. create a symbolic link beast2 -> BEAST2/workspace/beast2/
  1. create Hudson project BEAST2-GUI through the web interface like for BEAST2 (only the web-part, not the symbolic link part).
  2. make sure that the Ant targets compile-all and junitb are added
  3. make sure the ‘Run Xvnc during build’ checkbox is checked.

Setting up Hudson for and add-on to BEAST2 

Add-ons can assume that beast2, and all other add-ons, are in the parent directory of the add-on. To achieve this on Hudson:

  • create Hudson project MYADDON through the web interface
  • set up Subversion, ant and junit test stuff
  • ssh into hudson machine and go to the directory /usr/share/tomcat6/.hudson/jobs
  • create a directory ‘myaddon’
  • goto /usr/share/tomcat6/.hudson/jobs/MYADDON
  • delete directory ‘workspace’

 sudo rmdir workspace

  • create symbolic link workspace -> ../myaddon

 sudo ln -s ../myaddon/ workspace

  • make directory myaddon accessible for Hudson

sudo chown tomcat6 ../myaddon
sudo chgrp tomcat6 ../myaddon

Note that the Hudson name of the add-on and the add-on itself are in different case.

Restarting Hudson

Log into and restart tomcat using sudo /etc/init.d/tomcat6 -restart.

Bayesian evolutionary analysis by sampling trees

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