Problems running OBAMA and ORC packages in BEAST2 on a Linux cluster

[Miller, Mark]

I have been trying to get OBAMA and ORC packages to run for CIPRES users.

I installed them outside of Beauti, as we using a large cluster.

When I run ./packagemanager -add ORC (or OBAMA)

It says they are already installed.

 

But when I run the test files, I get the error appended below.

I wonder if anyone has a suggestion?

 

Thanks
Mark

 

Error 1017 parsing the xml input file

Class could not be found. Did you mean beast.evolution.operators.AttachOperator?

Perhaps a package required for this class is not installed?

Error detected about here:

  <beast>

      <run id='mcmc' spec='MCMC'>

          <operator id='AdaptableOperatorSampler.ucldStdev' spec='orc.operators.AdaptableOperatorSampler'>

[Miller, Mark]

Dear all,

 

I solved this issue, and will report the solution here for the record, in case other with my level of (in)experience will benefit.

I installed the packages in the appropriate directory on our cluster using git clone.

However, this did not provide .jar files that are required.

ORC on github does not have a .jar file, so we created it.

OBAMA had one, we just dropped it in the directory.

 

It’s all working now.

 

Best,

Mark

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