Plot EBSP output from BEAST 2?

[Amy]

Hi BEAST users,

I have run Extended Bayesian Skyline Plots in BEAST2 via the CIPRES Science Gateway and viewed the results in Tracer, but I am stumped on how to plot the output. My understanding is that BEAST 2 produces a separate EBSP log file that can be plotted in EBSPAnalyser (instead of a csv file that could be plotted using python as in BEAST 1), but I cannot figure out how to operate EBSPAnalyser. I've seen Remco's response to a similar inquiry posted a while back:

"For BEAST 2.0.2, if you locate the beast.jar file in BEAST, you can run the EBSPAnalyser from the command line using 
java -cp $(dir)/beast.jar beast.app.tools.EBSPAnalyser 
where $(dir) points to the directory where beast.jar is located. A window pops up where you specify the log file and some other settings."

However, when I try this, I get the following error message:

Exception in thread "main" java.lang.NoClassDefFoundError: beast/app/tools/EBSPAnalyser

Caused by: java.lang.ClassNotFoundException: beast.app.tools.EBSPAnalyser

at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

Is my problem that I haven't compiled the file correctly (in which case, can someone explain how to do that)? Is there another trick to getting EBSPAnalyser to work? Thanks in advance for any insights anyone can provide.

Amy

[Remco Bouckaert]

Hi Amy,

Perhaps there is a problem with setting up the path, which can be a bit tricky if there is a space in the path name. You could try the following: open a terminal, change directory to where beast.jar is (the lib directory where you installed BEAST) and then use

java -cp beast.jar beast.app.tools.EBSPAnalyser

from that directory.

Hope this helps,

Remco