GenePattern 3.9.7 Release Notes

Released April 5, 2016

GenePattern 3.9.7 requires Java 7+.

System requirements and known issues are detailed on the following pages. 

Bug Fixes & Enhancements

  • Better retry handling in queueing system integration. Fixes "error getting status for job" failure.
  • Fixed bug that interfered with uploading two GenomeSpace files in a row.
  • Better handling of file paths containing special characters in pipeline jobs.

Admin Support

  • Command line substitutions for modules can now be defined in the YAML configuration.
  • GenomeSpace username and token can now be used to authenticate when using the REST API.

Modules Released Since Jan. 22, 2016

  • ExpressionFileCreator - Updated to make use of the R package installer. Fixed a bug in failing to remove downloaded annotation files. (Beta)
  • HeatMapViewer - A configurable JavaScript, in browser, heat map viewer that provides users with several options for manipulating and visualizing array-based data. (Beta)
  • GSEA - Updated to provide access to MSigDB v5.1.
  • GSEAPreranked - Updated to provide access to MSigDB v5.1.
  • ssGSEAProjection - Updated to provide access to MSigDB v5.1.
  • MutSigCV - Updated for portability. (Beta)