Modified Globus classes to use multipart upload/moves to S3 to better handle files > 5gb

GenePattern installation instructions

Identical to b439. Created just to test github action updates that trigger on a new release

Add upload module zip api method.
Fix for search api
Updated visualizer utils for launcher modules
remove exclusion clause for new jobs run (?)
added stats about guest users seperately in weekly report
Addtional logging statements
Fix for globus bug
added job id to launch URL

test

B429

User Interface: misc language improvements
User Interface: GP-9756 files tab now retains position in scroll across pages
User Interface: New Feature - GP-9757 can now name jobs by adding a tag to a job formatted as "name=somename" or jobname="somename"
REST API: GP-9808, added a method to DataResource to allow javascript visualizers to create output files and save them back to the server
Server Administration: Changed security so that all module documentation is visible without a login

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'

User Interface: misc language improvements
User Interface: GP-9756 files tab now retains position in scroll across pages
User Interface: New Feature - GP-9757 can now name jobs by adding a tag to a job formatted as "name=somename" or jobname="somename"
REST API: GP-9808, added a method to DataResource to allow javascript visualizers to create output files and save them back to the server
Server Administration: Changed security so that all module documentation is visible without a login

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'

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'

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'

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'

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'