Difference between revisions of "Download and Installation"
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=geWorkbench 2.0.0 - System Requirements=
 +
==Java==   
 +
The Java 6 Runtime Environment (JRE6) is required.  For Windows and Linux, geWorkbench is distributed in two installer forms, one with and one without the JRE6 included.  To install a version of geWorkbench that does not include the JRE, the JRE must be installed separately on the machine.  On MacOSX, the Java 6 JRE is included with MacOSX versions 10.5 and higher. Please note that Java 6 is, in places, referred to by Sun as Java 1.6.  geWorkbench can run on both 32-bit and 64-bit versions of Java on appropriate OS platforms.
  
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=Software Requirements=
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The JRE6 can be downloaded from http://java.sun.com/javase/downloads/index.jsp.
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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.
 
  
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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.
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==Memory== 
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At least 2 GB is recommended.  geWorkbench 2.0.0 by default will request up to 1 GB of memory for the Java VM.
 +
       
 +
==Operating System==
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* '''Windows XP/Vista/Windows 7 (32 or 64-bit)''': no special requirements.
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* '''MacOSX''': Version 10.5 or higher is required to provide the Java 6 JRE.
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* '''Linux''': no special requirements known.
  
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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.
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geWorkbench, unless otherwise noted for particular components, can be run on both 32 and 64-bit operating systems and JREs.
  
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=Hardware Requirements=
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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.  
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=Installers=
 +
All three platform-specific versions of geWorkbench (Windows, Linux, and Macintosh) provide an installation wizard(generated using InstallAnywhere).  The installation download for these versions of geWorkbench include the word  "installer" in their name.
 +
   
 +
A generic version of geWorkbench, which does not use any installer, is also available.
  
  
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=Community Support Forums=
 
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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=
 +
 +
==Windows (XP/Vista/Windows 7)==
 +
   
 +
===Special note for Vista/Windows 7===
 +
If you run the installer on Vista or Windows 7, please install geWorkbench to your root directory, e.g. '''c:\geWorkbench_2.0.0'''  rather than to C:\Program Files\geWorkbench_2.0.0.
 +
 +
===Installer with JRE6===
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* File: geWorkbench_v2.0.0_Windows_installer_with_JRE6.exe
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* Includes the 32-bit Sun Java 6 JRE.
 +
 +
Download and double-click the installer file to begin installation.
 +
 +
===Installer without JRE6===           
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* File: geWorkbench_v2.0.0_Windows_installer_noJRE.exe
 +
* No JRE is included, you must make sure that an appropriate Java 6 JRE is installed on your system before installing geWorkbench.
 +
 +
Download and double-click the installer file to begin installation.
 +
 +
 +
==MacOSX==
 +
 +
File: geWorkbench_v2.0.0_MacOSX_installer.zip.
  
 +
This version relies on the Java 6 JRE included with recent updates to the MacOSX operating system.
  
−
=Installation Instructions=
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Double-click geworkbench_v2.0.0_MacOSX_installer.zip to begin installation.
  
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==Java Environment==
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===Notes===
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* Requires Mac OS X 10.5 or later
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* The compressed installer should be expanded automatically by the system.
  
−
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.
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==Linux==
  
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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.  
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===Installer with JRE6===
 +
File: geWorkbench_v2.0.0_Linux_installer_with_JRE6.bin.
  
−
Here is an example of setting the two environment variables for a JRE installed in the directory /opt:
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Includes the 32-bit Sun Java 6 JRE.
  
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JAVA_HOME=/opt/jre1.5.0_15
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===Installer without JRE6===
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File: geWorkbench_v2.0.0_Linux_installer_noJRE.bin.
  
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PATH=/opt/jre1.5.0_15/bin:$PATH
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===Installation===
  
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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.
  
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==geWorkbench Versions==
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After downloading, cd (if needed) to the directory to which you downloaded the installer.
  
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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.
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To begin the installation, type the command:
  
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===1. Windows (tested on XP/Vista)===
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"sh ./geWorkbench_v2.0.0_Linux_installer_with_JRE6.bin".
  
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'''File: geWorkbench_v1.8.0_Windows_installer_with_JRE1.5.exe'''
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This will extract geWorkbench into a new directory called geWorkbench_2.0.0.  
  
 +
To run geWorkbench, and assuming you are using the Linux bash shell, issue the command: 
 +
         
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"./rungeWorkbench_2.0.0"
  
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'''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.
 
  
 +
==Generic==
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A non-installer-based version of geWorkbench is supplied in a Zip file which should work on any platform.
  
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This version includes its own private copy of the Java 1.5 JRE bundled in, which avoids any potential problems with other Java versions.  
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File: geWorkbench_v2.0.0_Generic.zip
  
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Download and double-click the selected file to begin installation.
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Installation:
 +
   
 +
Unzip the file. It will create a directory geWorkbench_2.0.0.
 +
         
  
 +
===Running geWorkbench (generic)===
  
 +
You must have the Java 6 JRE installed and the JRE must be in the path for geWorkbench.
  
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===2. MacOSX===
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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".
 +
     
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Any: Alternatively, if you have Apache Ant installed, you can type "ant run" in the geWorkbench directory.
  
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'''File: geWorkbench_v1.8.0_MacOSX_installer.zip'''
 
  
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This version relies on the Java 1.5 JRE included with the MacOSX operating system. 
 
  
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*After downloading, double-click geworkbench_v1.8.0_MacOSX_installer.zip
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=Java Environment Configuration=
  
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*Notes
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To run a version of geWorkbench that does not include the Java 6 Runtime Environment (JRE6), the JRE6 must be installed and configured separately.
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**Requires Mac OS X 10.4 or later
 
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**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.
 
  
 +
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.
  
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===3. Linux===
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Here is an example of setting the two environment variables for a JRE installed in the directory /opt:
  
−
'''File: geWorkbench_v1.8.0_Linux_installer_with_JRE1.5.bin'''
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JAVA_HOME=/opt/jre1.6.0_20
  
−
This version includes its own private copy of the Java 1.5 JRE bundled in, which avoids any potential problems with other Java versions.  
+
PATH=/opt/jre1.6.0_20/bin:$PATH
  
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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.
 
  
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* 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.
 
  
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====Typcial steps in running X-windows====
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=Typical 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.
 
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.
  
Line 102: Line 149:
 
# allow remote connections with a command such as "xhost +".
 
# 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.
 
  
 +
=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.
  
−
====Running geWorkbench under Linux====
+
The forums can be viewed at https://cabig-kc.nci.nih.gov/Molecular/forums/
−
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.
 
−
           
 
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* 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"
 
−
     
 
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* Any: Alternatively, if you have Apache Ant installed, you can type "ant run" in the geWorkbench directory.
 
  
  

Revision as of 14:36, 10 June 2010

Download Instructions | License Information



This section contains instructions for downloading and installing geWorkbench.


geWorkbench 2.0.0 - System Requirements

Java

The Java 6 Runtime Environment (JRE6) is required. For Windows and Linux, geWorkbench is distributed in two installer forms, one with and one without the JRE6 included. To install a version of geWorkbench that does not include the JRE, the JRE must be installed separately on the machine. On MacOSX, the Java 6 JRE is included with MacOSX versions 10.5 and higher. Please note that Java 6 is, in places, referred to by Sun as Java 1.6. geWorkbench can run on both 32-bit and 64-bit versions of Java on appropriate OS platforms.

The JRE6 can be downloaded from http://java.sun.com/javase/downloads/index.jsp.

Memory

At least 2 GB is recommended. geWorkbench 2.0.0 by default will request up to 1 GB of memory for the Java VM.

Operating System

  • Windows XP/Vista/Windows 7 (32 or 64-bit): no special requirements.
  • MacOSX: Version 10.5 or higher is required to provide the Java 6 JRE.
  • Linux: no special requirements known.

geWorkbench, unless otherwise noted for particular components, can be run on both 32 and 64-bit operating systems and JREs.


Installers

All three platform-specific versions of geWorkbench (Windows, Linux, and Macintosh) provide an installation wizard(generated using InstallAnywhere). The installation download for these versions of geWorkbench include the word "installer" in their name.

A generic version of geWorkbench, which does not use any installer, is also available.


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



Installation Instructions

Windows (XP/Vista/Windows 7)

Special note for Vista/Windows 7

If you run the installer on Vista or Windows 7, please install geWorkbench to your root directory, e.g. c:\geWorkbench_2.0.0 rather than to C:\Program Files\geWorkbench_2.0.0.

Installer with JRE6

  • File: geWorkbench_v2.0.0_Windows_installer_with_JRE6.exe
  • Includes the 32-bit Sun Java 6 JRE.

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

Installer without JRE6

  • File: geWorkbench_v2.0.0_Windows_installer_noJRE.exe
  • No JRE is included, you must make sure that an appropriate Java 6 JRE is installed on your system before installing geWorkbench.

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


MacOSX

File: geWorkbench_v2.0.0_MacOSX_installer.zip.

This version relies on the Java 6 JRE included with recent updates to the MacOSX operating system.

Double-click geworkbench_v2.0.0_MacOSX_installer.zip to begin installation.

Notes

  • Requires Mac OS X 10.5 or later
  • The compressed installer should be expanded automatically by the system.

Linux

Installer with JRE6

File: geWorkbench_v2.0.0_Linux_installer_with_JRE6.bin.

Includes the 32-bit Sun Java 6 JRE.

Installer without JRE6

File: geWorkbench_v2.0.0_Linux_installer_noJRE.bin.

Installation

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.

After downloading, cd (if needed) to the directory to which you downloaded the installer.

To begin the installation, type the command:

"sh ./geWorkbench_v2.0.0_Linux_installer_with_JRE6.bin".

This will extract geWorkbench into a new directory called geWorkbench_2.0.0.

To run geWorkbench, and assuming you are using the Linux bash shell, issue the command:

"./rungeWorkbench_2.0.0"


Generic

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

File: geWorkbench_v2.0.0_Generic.zip

Installation:

Unzip the file. It will create a directory geWorkbench_2.0.0.


Running geWorkbench (generic)

You must have the Java 6 JRE installed and the JRE must be in the path for geWorkbench.

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.


Java Environment Configuration

To run a version of geWorkbench that does not include the Java 6 Runtime Environment (JRE6), the JRE6 must be installed and configured separately.

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/jre1.6.0_20

PATH=/opt/jre1.6.0_20/bin:$PATH


Typical 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 +".


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/


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.

Retrieved from "http://wiki.c2b2.columbia.edu/workbench/index.php?title=Download_and_Installation&oldid=6283"