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v3.9_21.11 build 363

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@bahill bahill released this 28 Oct 15:45
v3.9_21.11_b363
95920d8

New Features & Bug Fixes

  • Job Status - GenePattern again correctly displays the content of HTML job outputs (for instance, as output by GSEA)
  • File Management - GenePattern now supports GLOBUS, allowing for faster and more reliable uploads of large files, as well as transfers of GenePattern output files back to a connected GLOBUS account.
  • File Management - GenePattern jobs may now use GenePattern Notebook Workspace files as input.
  • File Management - GenePattern jobs may now use S3 URLs as input.
  • Job Submit Form - GenePattern is now case insensitive when evaluating file extensions.
  • Job Submit Form - In the properties panel, a module's 'current files' are once again correctly displayed.
  • Module Integrator - Job Options, such as memory and CPU, can now be specified when creating modules.*
  • Server Administration - The GenePattern server can now be an OpenID client to authenticate users.
  • Server Administration - To correctly allocate compute note memory in AWS, now provide memory/cpu as a resourceRequirement rather than as a containerOverride.
  • Server Administration - On AWS the ability to provide shared_data (server file paths) is again supported.
  • Server Administration - Documentation for running GenePattern in Docker on Windows has been improved.

*Note that createModule privileges are also needed for module editing in general.

Prerequisites for Installing GenePattern

  • Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
  • Docker

Installing and upgrading GenePattern via Docker

This is now the recommended method for a local GenePattern installation.
Please see our website for installation instructions

Mac OS X Install - GenePattern as an app

Make sure you do not have Java 11 installed. Switching and disabling will not work.
Download the GPserver.app.zip file. Unzip, drag the GenePattern.app file to your Applications folder, then launch the application. You will be prompted to enter some basic configuration details and the application will terminate. Restart and you are up and running.
The user data and customization files will be added to the ~/.genepattern hidden folder in your home directory.
Should you need to delete GenePattern - simply delete the GenePattern.app file from your Applications folder, and remove the ~/.genepattern directory as well.

Note: GenePattern is currently experiencing Apple certificate issues. To install GenePattern you may need to enable applications from third-party developers. See the instructions here. Alternately you can launch GenePattern from a terminal window by going to the directory /Applications/GenePattern.app/Contents/Resources and executing the GenePatternServer executable located there.

Linux Install

Download the 'GPserver.bin' file. Then run the installer in headless mode.

Instructions can be found in '/gp_home/resources/installer_example.properties'

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