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Installation

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Alex Zarebski edited this page May 6, 2022 · 3 revisions

Installation

You can install TimTam via BEAUti or by compiling it from source and installing the package yourself. Unless you are interested in actually developing the package, the BEAUti based solution is probably the one you want to use.

Install with BEAUti

  1. Download and install BEAST2.
  2. Launch the BEAUti application distributed with BEAST.
  3. From the File menu select “Manage Packages”.
  4. Click the “Package repositories” button at the bottom of the Package Manager dialog box.
  5. Select “Add URL” and enter the following URL: https://aezarebski.github.io/timtam/package.xml.
  6. Click the “Done” button, then select “timtam” from the list of packages.
  7. Click the “Install/Upgrade” button. Once installation is complete, XML files using timtam can be run from BEAST2.

Building from source

This option is primarily of interest for those interested in modifying the TimTam package.

Create a directory for BEAST2 and TimTam

Since the ant build scripts expect BEAST2 to be in a particular location, it is probably easiest to start by cloning a fresh copy of BEAST2 into a sensible directory created for this purpose.

$ mkdir foobar
$ cd foobar

Clone and compile BEAST2

$ git clone [email protected]:CompEvol/beast2.git
...
$ cd beast2
$ ant
...
$ cd ..

Clone and compile TimTam

$ git clone [email protected]:aezarebski/timtam2.git
...
$ cd timtam2
$ ant
...
$ cd ..

Note that in the output it should tell you that the jar file has been created: ./dist/timtam.v0.1.0.zip. We will need this later.

Install TimTam where BEAST2 can find it

You can use BEAUti to find where BEAST2 looks for packages, typically if you are using version 2.6 this will be in ~/.beast/2.6/.

$ java -cp ./beast2/build/dist/beast.jar beast.app.beauti.Beauti

Move the zip file to this location and unzip it there.

$ cd ~/.beast/2.6/
$ mkdir timtam
$ cd timtam
$ unzip -o <path/to/timtam.v0.1.0.zip>
...
$ cd <path/to/foobar>

Remco Bouckaert has an excellent blog post describing this process in more detail. Don’t forget to clear the Class Path in BEAUti before looking for the package!

Test one of the example XML files runs

You can test that the installation has worked by running one of the examples.

$ java -cp ../beast2/build/dist/beast.jar beast.app.beastapp.BeastMain examples/ex1.xml
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