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CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
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StarBeast and Standard template missing #435

Closed rbouckaert closed 8 years ago

rbouckaert commented 8 years ago

On Windows, with STACEY installed, the STACEY template shows up but Standard and StarBeast templates are missing from the File/Templates menu. They can be used by finding them through the File/Templates/Other menu. Below the BEAUti log after start up.

Loading package STACEY v1.0.4 Probing: stacey.jar Skip loading file:/C:/Users/Work/BEAST/2.3/STACEY/lib/stacey.jar: contains class stacey.BirthDeathCollapseModel that is already loaded Loading template C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\Standard.xml Investigating C:/Users/Work/AAA/biology/SoftWare/BEAST.v2.3.1 Processing C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\ClockModels.xml Processing C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\ParametricDistributions.xml Processing C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\StarBeast.xml Processing C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\SubstModels.xml Processing C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\TreePriors.xml Investigating /C:/Users/Work/BEAST/2.3/STACEY Processing C:\Users\Work\BEAST\2.3\STACEY\templates\STACEY.xml Investigating . Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1.\templates\ClockModels.xml since ClockModels.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1.\templates\ParametricDistributions.xml since ParametricDistributions.xml is already processed Processing C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1.\templates\Standard.xml Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1.\templates\StarBeast.xml since StarBeast.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1.\templates\SubstModels.xml since SubstModels.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1.\templates\TreePriors.xml since TreePriors.xml is already processed Investigating /C:/Users/Work/AAA/biology/SoftWare/BEAST.v2.3.1 Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\ClockModels.xml since ClockModels.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\ParametricDistributions.xml since ParametricDistributions.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\StarBeast.xml since StarBeast.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\SubstModels.xml since SubstModels.xml is already processed Skipping C:\Users\Work\AAA\biology\SoftWare\BEAST.v2.3.1\templates\TreePriors.xml since TreePriors.xml is already processed connect => beast.app.beauti.BeautiConnector subtemplate => beast.app.beauti.BeautiSubTemplate Uniform => beast.math.distributions.Uniform Normal => beast.math.distributions.Normal OneOnX => beast.math.distributions.OneOnX LogNormal => beast.math.distributions.LogNormalDistributionModel Exponential => beast.math.distributions.Exponential Gamma => beast.math.distributions.Gamma Beta => beast.math.distributions.Beta LaplaceDistribution => beast.math.distributions.LaplaceDistribution InverseGamma => beast.math.distributions.InverseGamma prior => beast.math.distributions.Prior map map map map map map map map map map map map beauticonfig fragment

run

Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537

template item TreeOperators is ignored PARTITIONS0:

[[], [], []] InPosterior=posterior prior likelihood Could not find plugin with id treeLikelihood.Species. Typo in template perhaps?

Validation message: At least one input of name 'xx' must be specified. class beast.core.MCMC != class beast.core.Runnable PARTITIONS0:

[[], [], []]

tgvaughan commented 8 years ago

Looks like the BEAST install directory was being included as a side-effect the behaviour that led to issue #95.

tanja819 commented 8 years ago

What is the correct set up in IntelliJ to ensure that the standard templates are loaded? I seem to be having the same problem which causes failures in a number of JUnit tests.

rbouckaert commented 8 years ago

You can set the "beast.install.dir" java directive (or environment variable) to the parent of the templates directory where the Standard.xml and StarBeast.xml files are (e.g. I have mine in /Users/remco/workspace/beast2) and they should be picked up from there.

Not sure how to do this in Intellij but I suppose setting up the debugger to include something like -Dbeast.install.dir=/Users/remco/workspace/beast2 as java argument (note, not as argument to the java class, but directly to java) should achieve this.

alexeid commented 8 years ago

Maybe we need a single page somewhere that describes how to set up IntelliJ so that BEAUti and the JUnit tests run?

On 1/12/2015, at 9:29 pm, Remco Bouckaert notifications@github.com wrote:

You can set the "beast.install.dir" java directive (or environment variable) to the parent of the templates directory where the Standard.xml and StarBeast.xml files are (e.g. I have mine in /Users/remco/workspace/beast2) and they should be picked up from there.

Not sure how to do this in Intellij but I suppose setting up the debugger to include something like -Dbeast.install.dir=/Users/remco/workspace/beast2 as java argument (note, not as argument to the java class, but directly to java) should achieve this.

— Reply to this email directly or view it on GitHub https://github.com/CompEvol/beast2/issues/435#issuecomment-161086259.

tgvaughan commented 8 years ago

I agree. This information could even be in the README, which is the traditional place to put compilation information. At least we should to link it from there.

Which unit tests are you seeing fail, @tanja819 ? There are two options that I like to use when running from an IDE: -Dbeast.install.dir=PATH_TO_BEAST_CODE and -Dbeast.user.package.dir=NONE. For the first of these I substitute the path to the root of the beast 2 directory (the parent directory of src/). The second I leave as-is, which causes beast to ignore any packages I have installed on my machine. (I don't want to be accidentally using a release version of some package.) Here's where you set these in the run configuration: runconfig