Download and Installation

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Download Instructions | License Information



This section contains instructions for downloading and installing geWorkbench.


Software Requirements

geWorkbench requires that the Sun Java 1.5 JRE be present on the local computer. The prebuilt Windows and Linux installer versions of geWorkbench (https://gforge.nci.nih.gov/frs/?group_id=78) include their own built-in copies of the Java 1.5 JRE. The Macintosh installer version relies on the Java 1.5 JRE that is included with the Macintosh OSX operating system.

A generic version of geWorkbench is also distributed that can be run on any platform. To run this version, the user will need to insure that the Java 1.5 JRE is present and will be used. The Java 1.5 JRE can be obtained from Sun's Java Web site, http://java.sun.com/j2se/1.5.0/download.jsp.

geWorkbench is known to have difficulties when run using Java 1.6. In particular, there is no connectivity to caArray when using Java 1.6. There are also other problems seen transiently. We recommend only a recent version of Java 1.5 be used.

Hardware Requirements

Testing of geWorkbench is done on machines with at least 2 GB of memory and this is now a suggested minimum configuration, though the program will work for many tasks with 512 MB. Working with large datasets (100s of arrays) will require the larger amount of memory.


IMPORTANT NOTICE ABOUT LICENSE

Use of geWorkbench is governed by the rules specified in the software license. Please make sure to read the license and understand your obligations before proceeding to download the application.


Downloads

Up-to-date versions of geWorkbench and the geWorkbench Software Development Kit can be downloaded from the project page at NCI's GForge repository: http://gforge.nci.nih.gov/frs/?group_id=78


Community Support Forums

geWorkbench community forums are operated by the caBIG Molecular Analysis Tools Knowledge Center. There are separate user and developer forums. Anyone can browse through existing postings, but to start a new topic one must first register.

The forums can be viewed at https://cabig-kc.nci.nih.gov/Molecular/forums/


Installation Instructions

Java Environment

The latest version of Java released by Sun is version 1.6 (Java 6). However, geWorkbench and other caBIG-related applications require use of Java 1.5. To avoid any confusion with later versions that may already be installed on a user's machine, the prebuilt Windows and Linux installers for geWorkbench include a private copy of the Java 1.5 JRE. The current Macintosh operating system, Mac OS X 10.5.2, includes the Java 1.5 JRE itself as the default version of Java.

geWorkbench is also available in a generic, platform independent version. To use this version, a copy of the Java 1.5 JRE must be installed on the machine and two environment variables must be properly configured. These are the JAVA_HOME and the PATH variables. They should be configured to point to your own installation of the JRE.

Here is an example of setting the two environment variables for a JRE installed in the directory /opt:

JAVA_HOME=/opt/jre1.5.0_15

PATH=/opt/jre1.5.0_15/bin:$PATH


geWorkbench Versions

Several different installation packages are available for this release of geWorkbench. Those with the word "installer" in the name included guided setup menus and are created using the InstallAnywhere program. An additional package, geWorkbench_v1.8.0_Generic.zip, requires the user to unzip the files and set two environment variables.

1. Windows (tested on XP/Vista)

File: geWorkbench_v1.8.0_Windows_installer_with_JRE1.5.exe


Special note for Vista - if you run this installer on Vista, please install geWorkbench to c:\geWorkbench_1.8.0 rather than to C:\Program Files\geWorkbench_1.8.0.


This version includes its own private copy of the Java 1.5 JRE bundled in, which avoids any potential problems with other Java versions.

Download and double-click the selected file to begin installation.


2. MacOSX

File: geWorkbench_v1.8.0_MacOSX_installer.zip

This version relies on the Java 1.5 JRE included with the MacOSX operating system.

  • After downloading, double-click geworkbench_v1.8.0_MacOSX_installer.zip
  • Notes
    • Requires Mac OS X 10.4 or later
    • The compressed installer should be recognized by Stuffit Expander and should automatically be expanded after downloading. If it is not expanded, you can expand it manually using StuffIt Expander 6.0 or later.


3. Linux

File: geWorkbench_v1.8.0_Linux_installer_with_JRE1.5.bin

This version includes its own private copy of the Java 1.5 JRE bundled in, which avoids any potential problems with other Java versions.

The Linux version of geWorkbench relies on X-Windows being installed and running. If you are running Linux on a server and e.g. Windows on your desktop, you will also need to run an X-windows server on your desktop machine.

  • Note - geWorkbench has only been tested running on a remote Linux server with the user's desktop machine running an X-server. geWorkbench has not been tested on a local Linux desktop machine.

Typcial steps in running X-windows

Here are some typical steps to configure a remote Linux host and a local desktop X-server. Under Windows, a local X-server can be provided for example by the Cygwin package.

On the remote Linux host (assuming you are using the bash shell), issue the command

  • "export DISPLAY=(your IP):0"

where (your IP) should be substituted with the IP address of your local desktop machine.

On your local desktop machine, you may need to

  1. start the X-windows server with a command such as "startx". You may need to cd to the X11 bin directory to find this command.
  2. allow remote connections with a command such as "xhost +".

Installing geWorkench under Linux

  • After downloading, cd (if needed) to the directory to which you downloaded the installer.
  • Type the command: "sh ./geWorkbench_v1.8.0_Linux_installer_with_JRE1.5.bin". This will extract geWorkbench into a new directory called geWorkbench_1.8.0.


Running geWorkbench under Linux

Assuming you are using the Linux bash shell, issue the command:

  • "./rungeWorkbench_1.8.0"


4. Generic

A non-installer-based version of geWorkbench is supplied in a Zip file which will work on any platform.

File: geWorkbench_v1.8.0_Generic.zip

Installation:

  • Unzip the file. It will create a directory geWorkbench1.8.0.


Running geWorkbench (generic):

  • Windows: you can double click on the file "launch_geWorkbench.bat" to launch geWorkbench, or run it from a command window.
  • Linux/Unix: Execute the script "launch_geworkbench.sh". You will need to have X-windows set up as describe above under section 3, Linux.
    • ". ./launch_geworkbench.sh"
  • Any: Alternatively, if you have Apache Ant installed, you can type "ant run" in the geWorkbench directory.


Tutorial data

tutorial_data.zip (3.586 MB) - data files in several different formats useful for the tutorials or just trying out geWorkbench.

Bcell-100.zip (5.256 MB) - A large (100 array) microarray dataset in the geWorkbench matrix format. Data is from the lab of Riccardo Dalla-Favera, Columbia University, and is provided only for use in learning and testing geWorkbench. It was obtained from experiments using Affymetrix HG-U95Av2 chips. This file contains the same data as the previously used file "webmatrix", but with the array subsets given more descriptive names.


Training Slides

A set of PowerPoint training slides for an earlier version of geWorkbench is still available. The PowerPoint file is available from the Project Documentation section of this site.

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