GenePattern 3.7.0 Release Notes

Released September 2, 2013

GenePattern 3.7.0 contains several new features and fixes.

Also see:

New Features

Simplified Publication of modules from GenePattern to GPARC

The GenePattern Module Integrator now offers direct publication of modules to GPARC (a GenePattern module repository and community where users can share and discuss their own modules).  Read more about the GenePattern/GPARC integration in our User Guide.


Enhanced File Input

Often a GenePattern module requires as input either a data file that may be (1) retrieved from a known public data repository or (2) provided by the user.  Prior to this release, the module author would need to defiine two optional input parameters: a choice parameter listing the set of files available from the public data repository and a file input parameter.  The module user would be required to provide input for one of these:


With this release, module authors can replace the pair of input parameters with a single input file parameter.  Module users can toggle between selecting a file from a drop-down list or uploading their own file.





 The input file parameter's drop-down list may be statically defined or populated dynamically (at run time).  The dynamic drop-down list is populated with a file listing from a remote ftp directory.  The module author specifies the URL of the remote ftp directory using the module integrator:

This enhanced file input feature will be employed in upcoming releases of the Cufflinks family of modules, and the RNASeQC and TopHat modules.


The 3.7.0 release contains a number of fixes and minor enhancements, including

  • Allow specification of URL for pipeline input file parameter 
  • Allow server file path inputs to visualizer when GenePattern server and client are not running on the same system
  • Eliminated run time errors that would occur when editing a provenance pipeline created from jobs with GenomeSpace input files
  • Fixed error in SGE (Sun Grid Engine) integration that resulted in an ERROR job status being returned when job completes successfully.