BEAST2 & BEASTvntr

Bayesian phylogenetic analysis of molecular sequences and VNTR or Microsatellites

• beagle-lib v2.1.2
• BEAST v2.4.7
• BEASTvntr v0.1.1

Building Docker BEAST2 and BEASTvntr

$ docker build -t beast-vntr .

Running GUI applications using Docker for Mac

Installing XQuarts

https://www.xquartz.org/

You might have to reboot your computer.

Configuring XQuarts

Start XQuartz from command line using:

$ open -a XQuartz

In the XQuartz preferences, go to the Preferences menu, then the Security tab, and enable Allow connections from network clients.

Run the following:

$ IP=$(ifconfig en0 | grep inet | awk '$1=="inet" {print $2}')
$ xhost + $IP

You should be seeing something like:

w.x.y.z being added to access control list

where w.x.y.z is your IP address.

Running BEASTvntr

$ docker run -it -e DISPLAY=$IP:0 beast-vntr

Known Issues

Running BEAUti throws the null pointer exception shown below:

java.lang.NullPointerException
	at beast.app.beastapp.BeastLauncher.copyFilesInDir(Unknown Source)
	at beast.app.beastapp.BeastLauncher.createBeastPackage(Unknown Source)
	at beast.app.beastapp.BeastLauncher.loadBEASTJars(Unknown Source)
	at beast.app.beauti.BeautiLauncher.main(Unknown Source)

References

• http://www.beast2.org/
• http://beast.community/
• https://github.com/CompEvol/beast2
• https://github.com/beagle-dev/beagle-lib
• https://github.com/arjun-1/BEASTvntr