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v 3.9_21.12 build 373

Pre-release
Pre-release

New Features & Bug Fixes since build 352 (July 2021)

  • 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.
  • File Management - Direct HTTP downloads no longer fail for users with spaces in their usernames.
  • 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 - Dynamic file lists may now use an Amazon S3 source.
  • Module Integrator - Job Options, such as memory and CPU, can now be specified when creating modules.*
  • Module Integrator - The GParc web app has been deprecated. Therefore users may no longer submit to GParc from the module integrator.
  • 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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Testing IA installer that only built Linux binary

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Testing installer

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Pre-release

This build is for internal testing only.

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v3.9_21.11 build 363

Pre-release
Pre-release

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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New Features & Bug Fixes

  • Module Integrator - Documentation can now be supplied by a publicly accessible URL.
  • Browser job notifications now correctly indicate when a job has completed successfully
  • Server Administration - The webserver log now only displays the last n lines of the log file - configurable by the admin user.
  • Server Administration - Issues with inputs for some modules (including HTSeq.Count & HISAT2Aligner) have been resolved.
  • Server Administration - The handling of remote directories has been improved, addressing issues with running MethylationCNVAnalysis.

*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'

134b810
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New Features & Bug Fixes

  • The What's New web tour has been updated to highlight recent new features.
  • Server Administration - Added the ability to allow the GP client upload and download files directly from AWS S3 using pre-signed URLs - This is now the default on our AWS hosted server (cloud.genepattern.org), and has improved the experience of uploading large files, among other administrative benefits.
  • Server Administration - GenePattern can now be installed on Windows 10 via WSL 2 and Docker.
  • Server Administration - allow.input.file.paths is now set to false by default in new installations.
  • Server Administration - For old modules using patches,(e.g. BowTie.aligner v 2.1.0) the GP server now correctly follows redirects to the patch repository.
  • Server Administration - Users with admin privileges can edit any module on the server by setting allowAdminEditNonLocalModules to true in the server's configuration yaml
  • Server Administration - Purging of jobs as well as uploaded and tmp data can now be configured at a more granular level. See '/resources/config_example.yaml' for details.
  • Server Administration - As of this release the R and MATLAB programming clients are deprecated. The Python & Java clients are still supported.
  • Job Submit Page - The properties panel now displays a link to the module's Docker image and source repository, where specified by the module.
  • Job Submit Page - The properties panel now correctly displays a link to the module license if one is present and specified.
  • Files Tab - The Files tab upload button has been restored to working order.
  • Module Integrator - It is now possible to change a module's privacy setting without incrementing its version.
  • Module Integrator - Choice lists for input files may now use https/https, as well as FTP.
  • Module Integrator - Choice lists for text input now allow for a blank default value.

*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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Build 322

Pre-release
Pre-release

Prerelease for testing

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Pre-release

New Features & Bug Fixes

  • On the module submit page, modules will not warn if the file input type provided is unexpected.
  • Pipelines are no longer cut off by the configured limit to concurrent jobs
  • The REST API has been updated to use the correct syntax for advanced job options (such as job.memory)

Prerequisites for Installing GenePattern

  • Java 8 or 9. Untested with Java 11.
  • Docker

Mac OS X Install

Download the GPserver.app.3.9_20.10.05_b293.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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New Features & Bug Fixes

  • Module Integrator - Users can now edit the modules they have uploaded to servers where they have createModule* privileges.
  • Module Integrator - Default Docker containers are now provided via a drop-down.
  • Module Integrator - Added the ability to create and edit parameter groups within the integrator.
  • Module Integrator - Improved handling of module parameter flags to prevent duplication on the command line.
  • Module Integrator - Added ability to edit without incrementing the version of a module.
  • Module Integrator - Added ability for admins to edit the LSID field.
  • Module Integrator - Updated help documentation.
  • Job Status Page - Congestion estimate in the pending state now lists the number of jobs ahead of yours.
  • File tab - Stale files can now be deleted from the Files tab

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

Prerequisites for Installing GenePattern

  • Java 8 or 9. Untested with Java 11.
  • Docker

Mac OS X Install

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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Pre-release
3.9_20.11.18_b305

fix for trying to lower case an array that is not a string