GenePattern 3.9.10 Release Notes

Released May 10, 2017

Release Notes - GenePattern - Version 3.9.10

New Tool

Visualizer Launcher -  a tool for launching Java applets on your desktop. We developed this tool as a work-around for the known issue that Java applet based visualizers no longer work in any browser.

More information about this tool, and the current state of visualizers in GenePattern, can be found in our blog post by clicking here.

Bug Fixes

  • [GPAT-2124] - JavaScript Visualizers unable to use GenomeSpace files as input
  • [GP-6191] - Improve error handling in R package installer wrapper script
  • [GP-6213] - Custom properties page, can't change property which is set in ''
  • [GP-6214] - Config_yaml file, can't change property which is set in ''

Minor Improvements and New Features

  • [GP-6435] - Change default job history to 15
  • [GP-6471] - Sort database schema files by version number
  • [GP-6475] - Make '' a configuration property
  • [GP-6476] - Remove 'input.file.mode' property
  • [GP-6486] - custom properties: would like to use the empty string as a value
  • [GP-6347] - Make the R 'site-library' a configuration parameter
  • [GP-6258] - Improve configuration of 'env-arch' substitution parameter

Modules Released or Updated Since February 6, 2017

ssGSEAProjection -  Updated to give access to MSigDB v6.0. Updated to use GenePattern native file lists. Fixes a bug to improve certain error messages.
GSEA - Updated to give access to MSigDB v6.0
GSEAPreranked - Updated to give access to MSigDB v6.0
FastQC - Full production release
removeSamples - Installed from GParc

Other Tools and Resources Released or Updated Since February 6, 2017

GenePattern Notebook Repository - The Repository has been updated to v17.05 and is now hosted on Amazon Web Services. Read more about this update in the release notes, by clicking here.