installing BEAST packages from command-line?

[carlo pacioni]

Hi Remco,

Is it possible to install BEAST packages from command-line rather than using BEAUti’s GUI.

 

I find myself in a very silly situation. I’m trying to get BEASTv2 up and running on Nectar Cloud (running Ubuntu 16). When I use sudo apt-get -y install openJDK-8-jdk to install java, BEAST is terminated the moment I disconnect from my SSH. I tried using nohup <command> &, TMUX or screen, but none of them worked.

 

When I use sudo apt-get -y install oracle-java8-installer to install java, I can disconnect from my SSH without BEAST being terminated, but I can’t open BEAUti in the GUI (which I could forward using X11-apps when java was installed as above).

 

I’m sure I’m missing something very basic here (and suggestions are welcomed!), but despite dedicating a fair bit of time I couldn’t figure this out…

 

Thanks,

Carlo

 

[Remco Bouckaert]

Hi Carlo,

There is a utility beast/bin/addonmanager that you can use to install packages.

Usage: addonmanager [-list] [-add <NAME>] [-del <NAME>] [-useAppDir] [-dir <DIR>] [-help] 

    -list List available packages

    -add Install the <NAME> package 

    -del Uninstall the <NAME> package 

    -useAppDir Use application (system wide) installation directory. Note this requires writing rights to the application directory. If not specified, the user's BEAST directory will be used.

    -dir Install/uninstall package in directory <DIR>. This overrides the useAppDir option

    -help Show help

Examples:

addonmanager -list

addonmanager -add SNAPP

addonmanager -useAppDir -add SNAPP

addonmanager -del SNAPP

There is more detail here: http://beast2.org/managing-packages/

Cheers,

Remco

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[carlo pacioni]

Thanks Remco!

carlo