Download and Installation

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Download Instructions | License Information


Software Requirements

To run geWorkbench you will need to have Sun Java J2SE 5.0 or higher installed on your computer (this is also referred to as the Java 1.5 JRE). If the JRE is not already installed on your computer you can get it from Sun's Java Web site, http://java.sun.com/j2se/1.5.0/download.jsp. geWorkbench is downloaded as a self-installing package with support for Windows, Linux and MAC OS-X.

geWorkbench is known to have difficulties when run using Java 1.6. We recommend only a recent version of Java 1.5 be used.

Hardware Requirements

Testing of geWorkbench is done on machines with 1 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) may require additional 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 (current version -> 1.5.1) and the geWorkbench Software Development Kit (current version -> 1.0.1) can be downloaded from the project page at NCI's GForge repository: 

  http://gforge.nci.nih.gov/frs/?group_id=78

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

You must have the Java 1.5 JRE installed before installing geWorkbench.

geWorkbench has been built and tested using Java 1.5, and this is the only recommended environment for running geWorkbench. There are known problems which occur if one attempts to run geWorkbench with Java 1.6.

If you have both Java 1.5 and Java 1.6 installed on your computer it can be difficult to ascertain which will be used when running one of the installer based versions of geWorkbench.

  • A Windows version of geWorkbench is supplied which includes its own private copy of the Java 1.5 JRE. This is the recommended installation for Windows. The file is geWorkbench_v1.5.1_Windows_installer_with_JRE1.5.exe. This eliminates any conflicts if Java 1.6 is also installed on the machine.
  • The remaining geWorkbench packages do not include the Java JRE.
  • For complete control of Java version, one can install the generic, non-installer version of geWorkbench. The file is geWorkbench_v1.5.1_Generic.zip. When using this installation, one can control the version of Java used by setting two environment variables: JAVA_HOME and PATH.

Example of setting environment variables:

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


geWorkbench Installation

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_v1.5.1_Generic.zip, requires the user to unzip the files and set two environment variables.

1. Windows (tested on XP/Vista)

File: geWorkbench_v1.5.1_Windows_installer_with_Jre1.5.exe - (recommended)

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

File: geWorkbench_v1.5.1_Windows_installer_noJRE.exe - You can use this file if you know you have Java JRE 1.5 already installed (and JRE 1.6 is NOT installed).

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


2. MacOSX

File: geWorkbench_v1.5.1_MacOSX_installer.zip

  • After downloading, double-click geworkbench_v1.5.1_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.
    • If you have any problems launching the installer once it has been expanded, make sure that the compressed installer was expanded using Stuffit Expander.


3. Linux

File: geWorkbench_v1.5.1_Linux_installer.bin.

To run the installation process or geWorkbench, you may need to set up several environment variables.

  • Example:
    • JAVA_HOME=/opt/jdk1.5.0_15
    • PATH=/opt/jdk1.5.0_15/bin:$PATH
  • Depending on the X Windows server you are running, you may also need to set your X Windows DISPLAY variable; the installer requires X windows to display installation status:
  • DISPLAY=(your IP):0
  • After downloading, cd to the directory where you downloaded the installer.
  • At the prompt type: sh ./install.bin (where install.bin is the name of the file you downloaded).


4. Generic

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

File: geWorkbench_v1.5.1_Generic.zip

Installation:

  • Unzip the file. It will create a directory geWorkbench1.5.1.


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".
  • 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 has been created which covers the basics of using geWorkbench plus several of the more advanced modules, such as Network Reverse Engineering and annotation retrieval. It follows the outline structure specified in the caBIG training guidelines. The PowerPoint file is available from the Project Documentation section of this site.

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