Revision as of 14:39, 29 October 2008

Software Requirements

geWorkbench requires 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 (current version -> 1.6.0) 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

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 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.