GenePattern 3.9.11rc-4+b216 Release Notes

Released May 20, 2019

Release Notes - GenePattern - Version 3.9.11rc-4+b216

The public GenePattern server hosted by the GenePattern team was officially migrated to the Amazon cloud: on January 1, 2019. To support this migration, GenePattern now requires that all modules be run in a Docker container.
More information about our use of Docker and the administration of GenePattern in the cloud can be found in our wiki on GitHub.

Please note that GenePattern releases are now hosted on GitHub along with our source code.

New Features and Improvements

  • [GP-7672] - GenePattern Notebooks catalog tab added to the left-hand panel
  • [GP-7712] - GenePattern Notebook information block added above the protocols 
  • [GP-7115] - FilePurger now removes files from the local file system and cleans up the corresponding files in S3 
  • [GP-7488] - Added a script to replace on local mac installs to allow modules to be run with singularity instead 
  • Added resources/ file for headless Linux install

Modules Released or Updated Since January 1, 2019

Kallisto - beta implementation. Intended to be used for RNA quantitation against a human index (Homo_sapiens.GRCh38.95_kalllisto_index).
PreprocessReadCounts renamed as VoomNormalize

Other Tools and Resources Released or Updated Since January 1, 2019

GenePattern Notebook Repository - The Repository was updated to v19.02 in February, and has just been updated to v19.05. Read more about these updates in the release notes, by clicking here.