GenePattern 3.3.3 Release Notes

Released October 3, 2011

GenePattern 3.3.3 contains several new features and fixes.

New Features

Batch Execution

This feature adds high-throughput capabilities to GenePattern, by allowing a user to run a "batch" of jobs from a directory of input files. Running a batch job has the same effect as running a single job for each input file in the list.  For more information about how to use batch execution in GenePattern, see this in-depth article.

New Input Parameter: Directory

This option allows users to pass a directory to a module as input.  Users must upload the files into the Uploads tab or select a directory via the server file path before the job can be run.  This works as input for any module that allows directories as input.

File Uploader

The file uploader function has been improved in this release to include the creation of subdirectories in the Uploads tab.  In addition, the user interface now shows all uploaded files and does not allow duplicate file names.

GenomeSpace Integration

Users of GenomeSpace can send files to the cloud-based GenomeSpace Data Manager and use Data Manager files as inputs to GenePattern modules.  GenomeSpace is still in early development at this time.  For more information about GenomeSpace, see the GenomeSpace User Guide.  GenomeSpace requires Java 6.

Oracle (Sun Grid Engine) Integration

This release of GenePattern includes a plug-in for submitting jobs to Sun Grid Engine (SGE), also known as Oracle Grid Engine.  See the SGE section of the resources/config_example.yaml file for more details. The SGE plug-in requires Java 6.

LSF Integration

This release of GenePattern includes a plug-in for submitting jobs to LSF.  LSF has been available for GenePattern since version 3.2.3, but this release integrates LSF into the installer.


The 3.3.3 release fixes issues in GenePattern, including:

  • Included the Java 6 JVM in the GenePattern installer.
  • Cleaned up the format of file paths, which were full paths with escaped characters on some platforms.
  • Updated the installer to set a default hostname for the GenePattern server that will work on all platforms.
  • Fixed a problem that sometimes failed to provide a working dropdown for newly uploaded files.
  • Fixed an issue that was preventing jobs on Job Results pages beyond the first from being sent to modules or saved.
  • Corrected a problem that resulted in the Job Results page occasionally not listing the correct jobs.
  • Updated the HSQL database to v. to correct a problem starting GenePattern on an NFS share.
  • No longer ignores the configuration allow.input.file.paths=true on some server types (such as Windows XP).
  • Implemented more graceful handling of empty input files.
  • Improved the Send to list options for uploaded and result files.

Known Issues

Known issues in GenePattern 3.3.3 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 3.3.3 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 3.3.3 only works with the default setting, input.file.mode=path.
  • Links to server file paths may not work when the path involves symbolic links.  Workaround: Do not use symbolic links.

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 October 2011, 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
  • Linux: Ubuntu 10.4, CentOS (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
  • Firefox 3.6 and 7
  • Chrome
  • Safari 5.0.5

Current technology versions: Following are the technology versions used in GenePattern 3.3.3.

  • Java 5 and/or 6
  • R 2.5.0
  • Perl 5.8.8