STARBEAST - package missing

[Suzanne Williams]

Dear BEAST users,

I would be very grateful for your help. I have used the STARBEAST template in BEAUTi to set up an xml file, which I am now trying to run on a server. I am coming up against something that seems like a bug. The programme starts, recording an error message: 

‘Could not find package 'BEAST.base' (typo perhaps?)’

Later on, I get a message: 

‘This XML requires the following package that is not installed: BEAST.base v2.7.3’ and then the run stops. 

I’ve looked on the list of packages and I can’t see any ‘BEAST.base’

I have set up a batch file with this text:

---------------------------------------------------------------------------------------

#!/bin/bash

#SBATCH --partition=week

#SBATCH --output=job%j.out

#SBATCH --mem-per-cpu=1G

#SBATCH --cpus-per-task=32

module load beast

packagemanager -useAppDir -add starbeast3

pacakagemanager -useAppDir -add beast.app

packagemanager -useAppDir -add BEASTLabs v2.0.0

packagemanager -useAppDir -add ORC v1.1.1

packagemanager -useAppDir -add SA

packagemanager -useAppDir -add BEAST.base

packagemanager -list

srun beast /XXX.xml

---------------------------------------------------------------------------------------

Does anyone have any solutions? I would be very grateful for some help!

Thanks very much,

Suzanne

[Jordan Douglas]

Hi Suzanne,

I have seen this issue before and it was related to the java environment. Java 17 azul build should be used ideally and this is included with the beast2 release in the jre folder. This may be a problem for the system administrator of your server to address. 

Note that you can generally run beast and install packages without any superuser previlages and without the need to rely on an admin by downloading the beast release and then running it directly from the command line beast/bin/beast and bin/packagemanager.  This way, beast should run directly out of the box and you won't need to load it as a module.

Hope this helps,

Jordan

[Suzanne Williams]

Dear Jordan,

I'm sorry - I've only just seen your reply. Many thanks for your help. It's all working now.

best wishes,

Suzanne

--
You received this message because you are subscribed to a topic in the Google Groups "beast-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/beast-users/kvbsbcRJ1m8/unsubscribe.
To unsubscribe from this group and all its topics, send an email to beast-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/409b2e33-bb60-4480-bad7-fe3b36ffc206n%40googlegroups.com.