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Releases: genepattern/genepattern-server

b409

20 Dec 18:45
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New Features:

Server Administration: Added new configuration parameter, "groups.always.shareable.to", a comma-delimited list of user-group names to include on all job sharing UIs (along with 'Administrators' and 'Public' which were already there by default.
Server Administration: Added cookie policy statement and release to login page

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'

b408

18 Dec 17:36
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b408 Pre-release
Pre-release

New Features:

Server Administration: Added new configuration parameter, "groups.always.shareable.to", a comma-delimited list of user-group names to include on all job sharing UIs (along with 'Administrators' and 'Public' which were already there by default.

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'

b407

18 Dec 15:07
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b407 Pre-release
Pre-release

New Features:

Server Administration: Added new configuration parameter, "groups.always.shareable.to", a comma-delimited list of user-group names to include on all job sharing UIs (along with 'Administrators' and 'Public' which were already there by default.

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'

v3.9_100323_b405

03 Oct 20:15
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Server Administration: Add failover job executor so that if a first executor fails during job start, the job can be retried on the next executor.

Prerequisites for Installing GenePattern
Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true
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'

v3.9_080823_b401

08 Aug 18:27
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v3.9_080823_b401 Pre-release
Pre-release

Release Candidate for August 8, 2023.
New Features & Bug Fixes since build 389 (November 2022)
• Server Administration - Added the ability for users to use GenePattern anonymously
• Server Administration - New system messages will always be shown once to users that have hidden the system message.
• Server Administration - To support GPUs in SLURM systems, can now allow users to select a partition and the # of GPUs to run GPU-backed analyses on
• Server Administration - Removed obsolete 'Advanced' tab from the Server Administration page.
• Server Administration - Fixed timestamps in GenePattern execution logs.
• Server Maintenance - Removed all reference to (no longer active) gpftp.broadinstitute.org site
• User Jobs - Fixed issue where missing optional parameters would cause jobs submitted via the REST API to not start..
• User Interface - restyled dropdown for multi-choice parameters (e.g. GSEA Gene Sets) to be wider to better display the choices

Prerequisites for Installing GenePattern
Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true
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'

b397

11 Jul 18:36
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Release Candidate for July 11, 2023.

New Features & Bug Fixes since build 389 (November 2022)
• Server Administration - Added the ability for users to use GenePattern anonymously
• Server Administration - New system messages will always be shown once to users that have hidden the system message.
• Server Administration - To support GPUs in SLURM systems, can now allow users to select a partition and the # of GPUs to run GPU-backed analyses on
• Server Administration - Removed obsolete 'Advanced' tab from the Server Administration page.
• Server Administration - Fixed timestamps in GenePattern execution logs.
• Server Maintenance - Removed all reference to (no longer active) gpftp.broadinstitute.org site
• User Jobs - Fixed issue where missing optional parameters would cause jobs submitted via the REST API to not start..
• User Interface - restyled dropdown for multi-choice parameters (e.g. GSEA Gene Sets) to be wider to better display the choices

Prerequisites for Installing GenePattern
Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true
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'

b389

29 Nov 15:55
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Release Candidate for November 29, 2022.

New Features & Bug Fixes since build 388 (August 2022)

  • Server Administration - Paths to server log files now displayed on log pages.
  • Server Administration - Fix for refreshing repositories causing admin pages fail to load
  • Server Administration - Improved error messages
  • Server Administration - Removed unnecessary logging
  • Server Administration - Fixed code to eliminate repetitive error messages about no no-arg constructors for DiskQuota and Memory classes
  • REST API - call to get list of user files tab contents.
  • User Interface - restyled dropdown for multi-choice parameters (e.g. GSEA Gene Sets) to be wider to better display the choices

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'

B388

18 Aug 20:29
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Release Candidate for August 9, 2022.

New Features & Bug Fixes since build 384 (June 2022)

  • Server Administration - Admins can now generate gp-unit tests directly from a job result.
  • Server Administration - Fix for downloading multiple files from a job delegated from a GenePattern server to another remote GenePattern server.
  • Server Administration - When a non-admin user adds for non-standard CPU or Memory for a job, instead of failing the job we now pick the next bigger standard value for CPU or Memory, or the max allowed value if the request is higher than the max allowed value.
  • Module Integrator - Added defaults and hints for CPU and Memory values.
  • Module Integrator - Can now delete a file at the same time as updating other module metadata.

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'

Build 387

09 Aug 20:56
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Build 387 Pre-release
Pre-release

Release Candidate for August 9, 2022.

New Features & Bug Fixes since build 384 (June 2022)

  • Server Administration - Admins can now generate gp-unit tests directly from a job result.
  • Server Administration - Fix for downloading multiple files from a job delegated from a GenePattern server to another remote GenePattern server.
  • Server Administration - When a non-admin user adds for non-standard CPU or Memory for a job, instead of failing the job we now pick the next bigger standard value for CPU or Memory, or the max allowed value if the request is higher than the max allowed value.
  • Module Integrator - Added defaults and hints for CPU and Memory values.
  • Module Integrator - Can now delete a file at the same time as updating other module metadata.

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'

Build 384

21 Apr 14:53
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Release Candidate for June 27, 2022.

New Features & Bug Fixes since build 377 (March 2022)

  • Globus - Better handle failed copies into GenePattern from Globus.
  • REST - Added detailed input parameter values & groups to the rest jobs endpoint.
  • Job Results - More accurate reporting of job queue waiting time.
  • Job Results - Creates a new log file that records elapsed time for jobs and input file sizes.
  • Job Results - Now displays a warning but allows access to job results when looking at the results page for a pipeline or module that was deleted after the run.
  • Job Results - Job results page now displays year as part of the date.
  • Server Administration - Updated to newer version of log4j to avoid vulnerabilities.
  • Server Administration - Updated start-genepattern.sh script for running docker on GenePattern to eliminate server registration loop.
  • Server Administration - Fix for remote jobs failing some getStatus calls when delegating to a different GenePattern server.
  • Server Administration - Fix for sometimes not downloading all files from a remotely executed job.
  • Server Administration - updates to permit dispatch to SLURM GPU queues.

Prerequisites for Installing GenePattern

Java 8 or 9. Note that GenePattern will not run if Java 11 is installed.
Docker
NOTE Our registration management is currently under development and will be updated with our next release.
Meanwhile, you can work around the need to register by adding this line to your
genepattern.properties file and restarting the server.
registeredServer=true

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'