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Installation

Requirements

Before installing Glotaran, please check to see if your system meets the specified requirements.

Please note that R is only supported up to version R 4.0.5, R 4.1.x is not yet supported.

Step 1: Installation

Glotaran can be downloaded from github. Note that there are different installers for each operating system (Windows, Mac OS X, Linux). Alternatively, a system independent zip distribution is also available which runs on any platform that has Java SE 8 installed.

Installation notes

Windows installation

Under newer versions of Windows it might not always be possible to install Glotaran in the "Programs" or "Program Files" folder without having elevated administrator rights. However, Glotaran can also safely be installed in for instance the Documents folder. Alternatively you can safely run the System Independent Zip distribution directly from your Downloads or Documents folder.

Linux installation

It might be necessary to make the installer executable. This can be done by issues the command chmod +x <file_name_of_the_installer> from the command line, or - depending on the Desktop Environment - right clicking the installer and selecting 'executable' from the properties dialog.

Mac OS X installation

Download the Glotaran Disk Image (dmg) from the website and open it. Then drag the Glotaran application to your application folder as normally.

Step 2: Configuration and set up

To make use of all of the functionality in Glotaran requires a working installation of R on the machine, with the R packages TIMP and Rserve installed. Otherwise you will not be able to run any new analysis, and only view existing results (such as the included demo project).

If you have not yet installed R, please refer to the official R-project website for instructions and install R, before proceeding with these notes.

Once R has been installed it is important to install the R packages TIMP and Rserve from CRAN from CRAN or alternatively rforge.net.

If needed, refer to the detailed instructions below.

Step 2a: Installing the R package TIMP

To install the R package TIMP , please take the following steps:

  1. Start R; either from the command line or start the R GUI
  2. Execute the following command: install.packages("TIMP")

Please note that TIMP version 1.13 or higher is required for Glotaran 1.5 and higher to run. The above command automatically install the latest stable version of TIMP.

Step 2b: Installing the R package Rserve

To install the R package Rserve, please take the following steps:

  1. Start R; either from the command line or start the R GUI
  2. Execute the following command: install.packages("Rserve")

Step 2c: Starting up Rserve

Windows set-up
Method 1: Starting Rserve from the R GUI

Other than the method described above, there is another way to start Rserve - from within the R GUI.

To start Rserve from the R GUI

  1. Start the 32-bit version of R (R i386; either from the command line or start the App)
  2. Execute the following commands:
    • library(Rserve)
    • and one of the following:
      • Rserve() (for Windows and Linux/Unix)
      • Rserve(args='--no-save')  (for Mac OS X)
      • Rserve(args='--no-save', debug=TRUE) (if you run into issues)
Method 2: Starting Rserve from the command line

This method may provide more diagnostic information when errors occur. Find the R installation location. Under Windows this is typically:

  • C:\Program Files\R\R-x.y.z

Next, locate the R library folder where the packages Rserve and TIMP have been installed in. Under Windows this is typically:

  • C:\Program Files\R\R-x.y.z\library (if you installed as administrator or with elevated rights)
  • %USERPROFILE%\R\win-library\x.y (otherwise)

Inside the R library folder navigate to the Rserve subfolder.

From the libs\i386 folder copy the following files from here:

  • Rserve.exe
  • Rserve_d.exe

To the i386 folder inside the bin folder of the R installation location, e.g.:

  • C:\Program Files\R\R-x.y.z\bin\i386

Note: depending on Windows settings you might not see the .exe extension (how to change that).

Now run the Rserve executable you just copied to the i386/bin folder from there, to see if it works. If you see a (Windows) Firewall dialog, please unblock the program. Rserve will not work otherwise.

Note you might want to make a shortcut to the Rserve.exe executable out it on your desktop so you can start it before you start Glotaran.

Linux and Max OS X set-up

Linux and Mac OS X require no special steps to setup. Start R (preferably from a terminal) and refer to method 1

Step 3: Starting Glotaran

Now you can start Glotaran from your application menu. Or, alternatively, you can start Glotaran using the glotaran executable in the bin sub folder of the Glotaran installation or zip folder.

You can also start Glotaran without starting Rserve first, but then you will not be able to run any new analysis, and only view existing results (such as the included demo project).

Step 4: Updating

This version of Glotaran is no longer actively maintained or updated, hence its rebranding to glotaran-legacy. However, if a new version is released you can find it on github.