GenePattern 3.3.2 Release Notes

Released June 1, 2011

GenePattern 3.3.2 contains several new features and fixes.

New Features

Upload for Large Input Files

This feature implements a new file upload system for handling input files larger than 2 GB. Users can now upload files before running a module by using the Upload Files button in the Uploads tab. An uploaded file can be used in any future analysis, by selecting a module in the drop-down list next to its name, by dragging and dropping the file onto a module input file field with the Specify File Path or URL radio button selected (Note: Internet Explorer does not support drag-and-drop), or by copying and pasting the file onto a module input field.

For more details on using large files in GenePattern, see this in-depth article.

Uploaded Datasets
Users can now view all files they have uploaded via the Upload Files button and use them in any future analysis under the Uploads tab on the main GenePattern page.


  • When users run a job with input files uploaded via the module run page, the job input files are stored with the job and are therefore scheduled to be purged 7 days after the job run, along with the job (on the Broad public server and on servers where the default time is in place). However, when users upload a file directly with the new large file upload feature, the files are not currently scheduled for deletion. Uploaded files must be manually deleted from the server. Please be aware of this and keep only those files on the server that you are currently using.
  • The feature added in 3.3.1 that allowed you to access Job Input Files in the Uploads tab has been deprecated. However, you can still see these files and copy/paste the link from the Job Status page.

Support for the Integrative Genomics Viewer (IGV) Visualizer

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. An IGV GenePattern module allows GenePattern users to easily visualize their GenePattern data in IGV through the standard GenePattern interface.

When users run the IGV module in GenePattern, they will see a new item on the Job Results page: a Launch button. Click the Launch button. You will be prompted by IGV for your GenePattern username and password in order to load the files into IGV. The latest version of IGV will download and open on your desktop with your GenePattern data loaded.


The 3.3.2 release fixes issues in GenePattern, including:

  • Updated the R client library to be compatible with R 2.10 and later
  • Fixed OutOfMemoryError when downloading large job results files

Known Issues

Known issues in GenePattern 3.3.2 include:

  • 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 3.3.2 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 StopGenePattnerServer.exe and select Run as administrator.
  • For GenePattern administrators who have changed the "input.file.mode" property (in the file) from default: GenePattern 3.3.2 only works with the default setting, input.file.mode=path.

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