GenePattern 3.9.9 Release Notes

Released February 6, 2017

This is a critical bug fix release required to install modules from the public module repository. This goes along with the new addresses for some GenePattern resources:

  • Module Repository URL:
  • Public Datasets:

Bug Fixes

  • [GP-6427] Fix Install from Repository page, set module repository URL to new address
  • [GP-6427] Secondary fix for installing patches from module repository
  • Update link to the Public Datasets
  • [GP-6360] Protocols page, update links to example data files
  • [GP-6360] Protocols page special-case for HTTP servers; automatically set href to match the protocol (http or https) of the GP server
  • [GP-6372] Fix broken link to the registrationURL
  • [GP-6254] Unable to view JsViewer tab in pipelines
  • [GP-6451] Optionally set HSQL_port in ''
  • [GP-6434] Pipeline Designer is throwing a $NULL error when handling large server file path inputs
  • [GP-6282] Enable 'job.priority' as a general JobRunner parameter
  • [GP-6280] Added 'resources' to built-in substitutions
  • [GP-6386] PostgreSQL: fix for "KEY" reserved word
  • [GP-6387] PostgreSQL: fix
  • [GP-6273] MySQL fix for timestamp columns with no default value
  • [GP-6272] Fix for missing log4j.jar file in Java GPClient library.

If you are updating from a previous version ...

Additional steps are required to get the 'Install from Repository' page to work.

step 1: Edit file

Set the *RepositoryURL(s) to use the new location. Make the following edits in your '' file. As usual, for best results, first shut down the server, then make the edits, then start the server.



Note: The DefaultPatchURL and DefaultPatchRepositoryURL properties are no longer required. Feel free to delete them from the file.


step 2: Update TASK_INSTALL.REPO_URL in the database

This step is only necessary if you installed modules on your server before updating to GP v3.9.9. It's only needed for the Source label and icon in the user interface, e.g. Production, Gparc, Beta, or Dev. Update the TASK_INSTALL.REPO_URL column in the database to match the newer urls. This example update statement was tested on Broad hosted servers with an Oracle database. 

-- Update statement 
update task_install set repo_url = 
    replace ( repo_url, '', '' )
where repo_url like ''



step 3: Update GP_USER_PROP['ModuleRepositoryURL'] in the database

As an additional step (not required) change the per-user 'ModuleRepositoryURL' setting. This example update statement was tested on Broad hosted servers with an Oracle database.

update gp_user_prop
    set value = replace (
        value, '', '') 
where key = 'ModuleRepositoryURL' 


Modues Released or Updated Since June 8, 2016

HierarchicalClusteringViewer - Initial Beta

ssGSEAProjection - Updated to give access to MSigDB v5.2. Updated to use GenePattern native file lists. Fixes a bug to improve certain error messages.

GSEAPreranked - Updated to give access to MSigDB v5.2.

GSEA - Updated to give access to MSigDB v5.2.

ComparativeMarkerSelectionViewer - Updated for new security restrictions in Chrome

DESeq2 - Initial Beta

Trimmomatic - Updated convert phred scores value to preserve no convert option in pipelines

CLSFileCreator - JavaScript implementation