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Changelog Summary

What's new in version:

Glotaran 1.3.0

  • Second major release
  • Built on the NetBeans RCP 7.3

Glotaran 1.2.0

Full changelog available here

Step 1: Installation

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

Glotaran can be downloaded from this location, see also the “Downloads” page on this website. Note that there are different installers for each operating system (Linux, Windows, Mac OS X, …). Alternatively, a System Independent Zip distribution is also available which runs on any platform that has Java 1.6 or greater installed.

Installation notes

Windows

Under certain versions of Windows it might not 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

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

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 / 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 it's dependencies and Rserve which are used by Glotaran. Refer to the instructions below how.

Step 2a: Installing the R-Package TIMP

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

  • Start R; either from the command line or start the R GUI
  • Execute the following command: install.packages("TIMP")
  • (Optional) To get the latest beta-version of TIMP, in addition run:
  • install.packages("TIMP", repos="http://R-Forge.R-project.org")

Please note that TIMP version 1.10 or higher is required for Glotaran 1.0 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:

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

Step 2c: Setting up Rserve

Windows

Locate the location where R has been installed. Under Windows this is typically: C:\Program Files\R\R-x.xx.xx This will henceforth be referred to as the “R installation folder”.

Next, locate the library folder where the packages Rserve and TIMP have been installed in. Under Windows XP this is typically: C:\Program Files\R\R-x.xx.xx\library or if you did not install the packages as administrator: <My Documents> R\R-x.xx.xx\library This will henceforth be referred to as the “R library folder

Inside the R library folder, navigate to the Rserve subfolder.

Copy the following files from here:

  • Rserve.exe
  • Rserve_d.exe

To the i386 folder inside the bin folder inside the R installation folder. Depending on the settings of Windows you might not see the .exe extension.

Under Windows XP this is typically located at: C:\Program Files\R\R-x.xx.x\bin\i386 or C:\Program Files\R\R-x.xx.x\bin\x64

Now run the Rserve executable you just copied to the i386/bin or x64/bin folder from there, to see if it works. If you see a (Windows) Fireall 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.

(alternative method) 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

  • Start R; either from the command line or start the RGui
  • Execute the following commands:
  • library(Rserve)
  • Rserve() (for Windows and Linux/Unix)
  • Rserve(args="--no-save") (for Mac OS X)

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

Glotaran will automatically periodically check for updates and will ask the user to install them. Alternatively it is possible to manually force an update-check by selecting 'Check for updates' under 'Help' in the application menu.

Future developments

In future version it will hopefully be possible to automate the above steps (installing TIMP, Rserve and running Rserve). Currently this is a work in progress; updates will be posted here.

installation.txt · Last modified: 2016/01/29 17:56 by jsnel