GenePattern 3.5.0 Release Notes

Released December 3, 2012

GenePattern 3.5 contains several new features and fixes.

New Features

License Support for Modules and Pipelines

GenePattern 3.5 supports the addition of end-user license agreements (EULAs) to modules and pipelines.  Module and pipeline creators can now attach EULA files to new versions of modules or pipelines.  Non-commercial users of these licensed modules/pipelines on either the Broad public server or private GenePattern servers need only accept the license for the version they are using, and their acceptance will be tracked at the Broad.  You need not view/accept EULA terms again unless the module/pipeline is updated.

Commercial users who want to use licensed modules should not accept EULAs that are targeted at academic and non-commercial communities.  In these cases, the licensing text will direct commercial users to contact the GenePattern team at and request a commercial EULA for the module or pipeline.


The 3.5 release fixes issues in GenePattern, including:

  • Improvements to the GenePattern UI, including revisions to the Recent Jobs and Uploads tabs and enhancements to the module listing to facilitate navigation.
  • Changing the help link on the module page to documentation to better reflect the content.
  • Improving the information provided in the error returned when jobs are terminated by the Load Sharing Facility that is used by public GenePattern Server due to insufficient memory.

Known Issues

Known issues in GenePattern 3.5 include:

  • There is a known issue regarding an update to the Java 6 platform which can cause problems for GenePattern users, specifically in using visualizer modules and the file uploader.  For more information, see this GenePattern blog entry.
  • There is a known issue regarding pipelines created in GenePattern 3.3.3 that have data files included and that have been imported to a new 3.5.0 server. If you are having problems with such a pipeline:

1. On the 3.5.0 server, select your pipeline and click edit to open it in the Pipeline Designer.
2. Click Save. You don't need to make any other changes to your pipeline.

  • There is a known issue with installing on OS X Lion (10.7) or on OS X Mountain Lion (10.8).  If you get an "Installation: Successfulnull" error or an error that looks like this:

1. Move Folder:              Destination: /Library/Frameworks/R.framework/Versions
WARNING - There was a problem copying /Library/Frameworks/R.framework/Versions/2.5

you may need to install R2.5 separately.  Download R2.5 from CRAN and follow the instruction in this section of the Administrators Guide.

  • There are known issues with installing on OS X Mountain Lion:
    • by default, Mountain Lion does not allow the installation of GenePattern because it is not from a "certified Apple Developer".  Workaround: Set Gatekeeper to allow applications to be installed from any source (see for more information).
    • if you select the option to install icons in the dock during install, the icons will not appear in the dock.  They will appear when the server is running.  Workaround: You can place them in the dock manually.
  • There is a known issue with Firefox 12 in Windows: When modules are installed from the repository, the page does not update after the modules are installed. It appears as if nothing happens, but going to the Manage Modules page should show that the modules were installed.
  • There is a known issues with Internet Explorer 9: Job Results page does not refresh automatically.  Workaround: Click the "compatibility mode" icon (looks like a broken page: Picture of the Compatibility View button (off) and when you click it, it will change from an outline to a solid color: Picture of the Compatibility View button (on)) in the toolbar and the page will refresh.
  • There are known issues with Safari 5.0.5 on MacOS X. To workaround these problems, install the latest version of Safari. First try software update. If you are still at version 5.0.5 or earlier:
  • There are known issues with Internet Explorer 8 and 9: The new drag and drop functionality of both the Module Integrator and Pipeline Designer is not available to them.  Workaround: Use a different browser, such as Firefox or Chrome.
  • ComparativeMarkerSelection Version 7 may fail when run on a GenePattern server installed in C:/Program Files (x86) on a 64-bit Windows machine. Other Java modules that invoke R with the command line " -DR=..." are likely to fail as well. Workaround: Either accept the GenePattern default install location of C:\GenePatternServer or, if you want to use C:/Program Files (x86), edit the R 2.5 Home setting on the Programming Languages page to change to the default GenePattern install location (C:\Program Files (x86)\GenePatternServer).
  • GenePattern does not support module names with spaces in them.  
  • Some GenePattern modules do not work when the input filename contains a space character. Workaround: Rename the input file without a space character.
  • On Macintosh: Java Runtime Environment (JRE) 1.6.0_15 does not work. Workaround: The GenePattern team suggests updating to the most recent JRE (GenePattern 3.4 has been tested with 1.6.0_20 and above).
  • On Windows 7/Vista: The StartGenePatternServer and StopGenePatternServer applications must be run as an administrator. To start or stop the GenePattern server, right-click on StartGenePatternServer.exe or StopGenePatternServer.exe and select Run as administrator.
  • For GenePattern administrators who have changed the "input.file.mode" property (in the file) from default: GenePattern 3.4 only works with the default setting, input.file.mode=path.

Hardware Requirements and Software Compatibility

Hardware requirements: GenePattern's hardware requirements are found on almost all currently available machines:

  • 256 MB RAM (individual modules may require additional RAM depending on the data being processed)
  • 500 MHz Pentium 3 or equivalent
  • Server space: 252 MB
  • Module space: As of December 2012, installing all GenePattern modules requires approximately 1 GB of hard drive space

Supported operating systems: GenePattern installers are available for Windows, Mac OS X, and Linux. GenePattern should work with any operating system that has a Java 5 or 6 virtual machine installed. We have tested it on the following OS platforms:

  • Windows: XP (32-bit and 64-bit), Windows 7/Vista (32-bit and 64-bit)
  • Mac: OS X 10.5, 10.6, 10.7, 10.8
  • Linux: Ubuntu 12.04, CentOS 5 (Note: these are only the platforms we test; GenePattern works on other Linux platforms as well)

Supported browsers: GenePattern has been tested on the following browsers:

  • Internet Explorer 8 & 9 (these do not support the Module Integrator and Pipeline Designer in GenePattern releases 3.4 and greater)
  • Firefox 16 & 17
  • Chrome
  • Safari 5.1+ (5.1+ required for Module Integrator and Pipeline Designer)

Current technology versions: Following are the technology versions used in GenePattern 3.5.

  • Java 5 and/or 6
  • R 2.5.0 (Included in Windows installs. Other versions of R can easily be installed to run with GenePattern modules as needed. See the Using Different Versions of R in-depth article for more information.)
  • Perl 5.8.8