Download GenePattern

No download is required to use GenePattern on the Broad public GenePattern server

GenePattern 3.9.3 (latest), Released: 2015-06-23

Linux (no VM) MacOSX (no VM)

Version (Build) Released Installers
3.9.3 (prod) 2015-06-23 Linux (no VM) MacOSX (no VM)
3.9.2 (prod) 2015-03-19 Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (VM) Windows (no VM) Windows_Pure_64_Bit (no VM)
3.9.1 (prod) 2015-01-16 Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (VM) Windows (no VM) Windows_Pure_64_Bit (no VM)
3.9.0 (prod) 2014-10-01 Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (VM) Windows (no VM) Windows_Pure_64_Bit (no VM)
3.8.2 (prod) 2014-09-02 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.8.1 (prod) 2014-04-07 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.8.0 (prod) 2014-01-06 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.7.3 (prod) N/A Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.7.0 (prod) 2013-09-02 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.6.1 (prod) 2013-07-01 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.6.0 (prod) 2013-06-03 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.5.2 (prod) N/A Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.5.0 (prod) 2012-12-03 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.4.1 (prod) N/A Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.4.0 (prod) 2012-09-03 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.3.3 (prod) 2011-10-03 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Windows (no VM) Windows (VM) warfile (no VM)
3.3.2 (prod) 2011-06-01 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Solaris (no VM) Windows (VM) warfile (no VM)
3.3.1 (prod) 2011-03-01 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Solaris (no VM) Windows (VM) warfile (no VM)
3.2.4 (prod) N/A Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Solaris (no VM) Windows (VM) warfile (no VM)
3.2.3 (prod) 2010-06-01 MacOSX (no VM) Windows (VM) warfile (no VM)
3.2.2 (prod) 2009-12-01 Linux (VM) Linux (no VM) MacOSX (no VM) Other Java Platforms (no VM) Solaris (no VM) Windows (VM) warfile (no VM)
1.4.0 (prod) 2005-06-01 Linux (no VM) Linux (VM) MacOSX (no VM) Windows (VM) Windows (no VM) warfile (no VM)
1.3.1 (prod) 2005-01-01 Linux (no VM) Linux (VM) MacOSX (no VM) Windows (VM) Windows (no VM) warfile (no VM)
1.3.0 (prod) 2004-12-01 Linux (no VM) Linux (VM) MacOSX (no VM) Windows (VM) Windows (no VM) warfile (no VM)
1.2.1 (prod) 2004-11-01 Linux (no VM) Linux (VM) MacOSX (no VM) Windows (VM)
1.2.0 (prod) 2004-07-01 Linux (no VM) Linux (VM) Linux_gpClient (VM) MacOSX (no VM) MacOSX (no VM) Windows (VM) Windows (VM)
1.1.0 (prod) 2004-04-01 Linux (VM) Linux (VM) MacOSX (no VM) MacOSX (no VM) Windows (VM)
1.0.0 (prod) 2004-03-01 Linux (VM) MacOSX (no VM) MacOSX (no VM) MacOSX (no VM) MacOSX (no VM) MacOSX (no VM) Windows (VM)

Installation Instructions

  1. Upgrading: If you are upgrading an existing GenePattern installation, see the FAQ for the recommended upgrade procedure.
  2. The FAQ contains critical information on preserving GenePattern settings and data. View the FAQ.
  3. Read the GenePattern License Agreement.
  4. Please check the hardware requirements and software compatibility page to see if your system will support installing and running GenePattern.
  5. View the Release Notes.

Start Installation

Click the Download link for your platform and save the file to your hard drive. To start the installation:

  • On Windows, double-click on the downloaded GPServer.exe file.
    Note: You must be logged on as an administrator to install software on Windows.
  • On Mac, double-click the downloaded zip file. After expanding the zip file, double-click GenePattern.
    Note: The default fields for R, Perl, and Java should not require changing, as they are set to the default location for Mac.
  • On Linux, open a shell, cd to the directory where you downloaded the installer, and at the prompt type:
    sh ./GPserver.bin
  • On other Java-enabled platforms, double-click on the downloaded GPServer.exe file.

Register

The first time the GenePattern server is launched, the GenePattern Registration page will appear in your browser.

Fill out the registration form, read the license agreement, and click the I Agree button at the bottom of the form.

View Server Installation Report

In the right-hand side of the GenePattern Configuration page, you will see a report summarizing the installation results. Note: Mac users will not see a log in the righthand pane.



If your summary contains errors other than those described below, there may have been problems with the installation. Please contact gp-help@broadinstitute.org.

  • On Linux, if R is not installed you will see the following errors:
    WARNING - There was a problem copying /usr/lib/R/library/GenePattern
    WARNING - Therre was a problm moving /usr/lib/R/library/GenePattern/runVisualizer.jar
    WARNING - Shortcut [for R] has no target
    ERROR - Unable to locate ASCII text file [for R] to be manipulated. Deferring...

Install Modules

Click the Install modules link. You will see the screen below, which lists the modules that are available.

Click Install Checked and all the available modules will be installed.




As each module is installed, a check mark appears in the far right column.



If a module requires additional software, you will be prompted to install the necessary software. For example, a number of modules require the MATLAB runtime component.

When a check mark appears next to the last module in the list, all of the modules have been installed.
 

Download Sample Datasets

Return to the GenePattern Configuration Page and click on the Download sample datasets link. You will see the screen shown below, providing links to sample datasets used in the GenePattern tutorial. To download a dataset, click on its link.


 

Log in to the GenePattern Server

Click 'Login and begin using GenePattern'.

You will see the home page of the GenePattern Web Client:



You are now ready to use GenePattern.

To learn more, view the video tutorial Getting Started (5 minutes) or the hands-on Quick Start (10 minutes) or Tutorial (40 minutes).

WAR file installation

The standard installation procedure uses the InstallAnywhere installer. For some installations, this mechanism is not appropriate (for example, when the platform is not supported or if the desire is to install into an existing web server and not use the Apache Tomcat installation created by the installer). In these situations, an alternative is to install GenePattern from a WAR file (Web ARchive), as described in Installing GenePattern from a WAR File.

Source Code

Source code for GenePattern is available under the GenePattern software license. Each module has a separate license provided by its author. For access to the source code, email the GenePattern team.


InstallAnywhere is a registered trademark of Flexera Software Corporation
Mac OS X is a registered trademark of Apple Computer, Inc.
Solaris and Java are trademarks of Oracle.
Windows is a registered trademark of Microsoft Corporation.

All other marks are properties of their respective owners.