Releases: genepattern/genepattern-server
b425
New Features:
Server Administration: Added tags to delegated jobs to make it easier to search as admin on job result page.
Server Administration: AltGP Job runner now adds tags with remote host, job and username to make searching on the remote host jobResults page easier
Server Administration: Update mysql jar file for mysql8
Server Administration: Moved target of server and user registration forms to shared google forms.
Server Administration: Trim lsids before comparison so make sure they match when downloading html results.
Server Administration: Update installer paths for RHEL9
User Experience: Added ability to have text fields with drop-down of values but still ability to enter custom values.
User Experience: Fixed resetting of values when reloading batch jobs.
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'
b409
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
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
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
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
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
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
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
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
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'