FAQ

How can I cite GenPlay?
If you like GenPlay and use it for your research, please help us by citing our publication in Bioinformatics:

Bioinformatics. 2011 May 19 GenPlay, a multi-purpose genome analyzer and browser. Lajugie J, Bouhassira E. Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA. PMID: 21596789

You can also link to GenPlay.net from your website to increase our visibility.

Thank you for your support!

How can I make sure I am using the last version of GenPlay ?
To be sure that you are not actually using an old version of GenPlay you need to delete the Java temporary files from the Java control panel. On Windows, the Java control panel is accessible from the Windows Control Panel > Java icon.

Where can I find the executable of GenPlay?
GenPlay can be launched from the Web Start page of this website.

The jar files of the current and past versions of GenPlay are available in the Older Versions section of this website.

Do I need a license to use GenPlay?
GenPlay is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Where can I download the source code of GenPlay?
The source code of GenPlay is available from the SVN repository at https://genplay.einstein.yu.edu/svn/GenPlay You can check out the latest source code with a SVN client with the following command: svn co https://genplay.einstein.yu.edu/svn/GenPlay

During zooming, the item I want to zoom in on keep sliding off the edge of the display. How should I use the zoom functionality to avoid this problem?
During the conception of the software we decided to handle this problem as follow:
 * A double click on a feature centers the screen on the selected feature.
 * A mouse wheel up or down zoom in or out on the feature that is at the center of the screen.  An unintended click on the mouse wheel starts the scroll mode which can be undesirable.

When I try to launch GenPlay on Mac OS I get the following message: "GenPlay is damaged and can't be opened. You should move it to the Trash". What should I do?
OS X Mountain Lion (10.8) has a new security feature called Gatekeeper. Gatekeeper is enabled by default and prevents applications distributed outside of the Mac App Store from launching.

Here is a workaround:
 * Open Gatekeeper settings located in "System Preferences > Security & Privacy"
 * Set "Allow applications downloaded from:" to "Anywhere" and confirm by pressing "Allow From Anywhere"
 * Download, unpack and run GenPlay
 * Once an application is successfully launched, it no longer goes through Gatekeeper. Thus you can restore Gatekeeper settings to the default option "Mac App Store and identified developers" after successfully launching the profiler

I have a Java error when I launch GenPlay, what do I do?
What is it?

In order to run a Java application, the computer needs to use a Java Runtime Environment (JRE). Many software install their own JRE, sometimes in their own directories, sometimes in the directory the JRE is supposed to be.

That can lead the operating system to get lost when it has to run Java applications and create incoherencies.

What to do then?

The main idea is to uninstall ALL JREs you have installed on your computer and to install the newer JRE ONLY.

Here is a fix for Windows:

In the best case, you will have to do the steps 1 and 4 only.

1. Go to "Control Panel" > "Programs and Features" and find the Java installation. Run the uninstall program for all of them.

You may experience an error when uninstalling meaning that you cannot fully uninstall the JRE. Then do step 2 and 3, skip them otherwise.

2. If it is the case, then you need to delete the folders manually.

For 32bits Windows, go to the folder:

C:\Program Files\Java

For 64bits Windows, go to both folders:

C:\Program Files (x86)\Java

C:\Program Files\Java

Delete all folders starting with "jre".

3. That is not a clean uninstall. In order to avoid issues in the future (especially when installing a newer JRE), you need to clean up the registry. Use a registry cleaner (such as CCleaner, Eusing Free Registry Cleaner, Wise Registry Cleaner ...).

This cleaning step is really important before installing a newer JRE.

4. Once ALL JREs uninstalled, download the latest Java version (here) and install it.

5. If the WebStart does not still work, please change the default software for opening ".jnlp" file. The system may have kept previous JRE version paths that are obviously not working anymore.

In order to change a default program, go to "Control Panel" > "Default Programs" > "Associate a file type or protocol with a program" and find the ".jnlp" extension and click the button "Change program…".

Go to the folder where the JRE is installed, then to the folder "bin" and select the file "javaws.exe".