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:
Additional steps are required to get the 'Install from Repository' page to work.
Set the *RepositoryURL(s) to use the new location. Make the following edits in your 'genepattern.properties' file. As usual, for best results, first shut down the server, then make the edits, then start the server.
DefaultModuleRepositoryURL=http://software.broadinstitute.org/webservices/gpModuleRepository ModuleRepositoryURL=http://software.broadinstitute.org/webservices/gpModuleRepository ModuleRepositoryURLs=http://software.broadinstitute.org/webservices/gpModuleRepository,\ http://software.broadinstitute.org/webservices/gparcModuleRepository,\ http://software.broadinstitute.org/webservices/betaModuleRepository DefaultSuiteRepositoryURL=http://software.broadinstitute.org/webservices/gpModuleRepository/suite SuiteRepositoryURL=http://software.broadinstitute.org/webservices/gpModuleRepository/suite SuiteRepositoryURLs=http://software.broadinstitute.org/webservices/gpModuleRepository/suite
Note: The DefaultPatchURL and DefaultPatchRepositoryURL properties are no longer required. Feel free to delete them from the file.
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, 'http://software.broadinstitute.org', 'http://www.broadinstitute.org' ) where repo_url like 'http://www.broadinstitute.org%' commit
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, 'www.broadinstitute.org', 'software.broadinstitute.org') where key = 'ModuleRepositoryURL' commit
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