Beagle PATH (partially) recognised on Ubuntu 22.04

Question

[Luca Arbore]

I have installed Beast 10.5 and for Beagle I have followed the instructions at https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions until step 3. export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH

I can run BEAST only in the same terminal window if I have have executed the export PATH command first. If I open a new terminal and try, I will get

Failed to load BEAGLE library: /home/alex/lib/libhmsbeagle-jni.so: libhmsbeagle.so.1: cannot open shared object file: No such file or directory BEAGLE not installed/found

Failed to load BEAGLE library: /home/alex/lib/libhmsbeagle-jni.so: libhmsbeagle.so.1: cannot open shared object file: No such file or directory
...
Creating BEAGLE DataLikelihood Delegate
Failed to load BEAGLE library: /home/alex/lib/libhmsbeagle-jni.so: libhmsbeagle.so.1: cannot open shared object file: No such file or directory
Fatal exception: No acceptable BEAGLE library plugins found. Make sure that BEAGLE is properly installed or try changing resource requirements.
java.lang.RuntimeException: No acceptable BEAGLE library plugins found. Make sure that BEAGLE is properly installed or try changing resource requirements.
at beagle.BeagleFactory.loadBeagleInstance(Unknown Source)
at dr.evomodel.treedatalikelihood.BeagleDataLikelihoodDelegate.<init>(Unknown Source)
at dr.evomodelxml.treedatalikelihood.TreeDataLikelihoodParser.createTreeDataLikelihood(Unknown Source)
at dr.evomodelxml.treedatalikelihood.TreeDataLikelihoodParser.parseXMLObject(Unknown Source)
at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.convert(Unknown Source)
at dr.xml.XMLParser.parse(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)

Any idea about what could cause such a behaviour? Thank you!

Answer 1

[GenoMax]

I can run BEAST only in the same terminal window if I have have executed the export PATH command first. If I open a new terminal and try

Variable (LD_LIBRARY_PATH) you are setting in step 3 is valid only in the terminal it was set in when it is exported on the command line like you are doing. In order to make it permanently available in all login/shell sessions you will need to add that export directive to your shell initialization file.

See more information here: https://tldp.org/LDP/Bash-Beginners-Guide/html/sect_03_01.html Depending on the shell you use this file will be different (e.g. .bashrc for bash etc). Once you add this line in, you will need to open a new terminal to see its effect. That will apply for each new shell session then on.