GenePattern 3.9.1 Released

GenePattern 3.9.1 is available for use on our Public GenePattern Server,  via download, and as an Amazon Machine Image (AMI)

New features include:
  • The ability to add tags and comments to jobs
  • An improved mechanism for using GenePattern data in IGV
  • Support for JavaScript based visualizers
We also made some user requested fixes and enhancements:

Full details about 3.9.1, including links to hardware & software requirements and known issues, can be found in our release notes.

Installing GenePattern on Mac OSX 10.9 (Mavericks) or 10.10 (Yosemite)
 
With Mac OS X 10.9 (Mavericks) Apple instituted a variety of application requirements that are incompatible with the GenePattern installer, which also apply to OS X 10.10 (Yosemite). As a consequence, those attempting to install GenePattern on Mavericks or Yosemite may encounter the following error message:

Despite this error message the GenePattern installer is not actually damaged. The message is part of a new Apple security measure. There are two options for working around this error and proceeding with a GenePattern installation, depending on your administrative privileges.
 
To determine if you have the appropriate admin privileges follow the instructions for If you have administrator privileges below. If the Allow apps downloaded from… text remains grayed out throughout the steps, it is unlikely that you have the necessary privileges. In this case, please follow the steps beneath If you do not have administrator privileges.
 
If you have administrator privileges
 
If you are an admin on your Mac computer you can temporarily disable the security settings that prevent GenePattern from being installed. To do this perform the following steps.
  1. Open System Preferences found in Applications > System Preferences
  2. Click on the Security & Privacy icon
  3. Click on the General tab
  4. In the bottom half of the window set Allow apps downloaded from… to Anywhere. If this section is grayed out you may first have to click the lock icon in the lower left corner of the window and enter your password.
  5. Start the GenePattern installer by double-clicking the downloaded file. Once GenePattern is installed the previous security settings may be reapplied.
If you do not have administrator privileges
 
Another possibility for installing GenePattern is to start the installer from the command line. To do this perform the following steps.
  1. Use the Terminal application found in Applications > Utilities to navigate to the Downloads directory and type "cd ~/Downloads"
  2. Find the GPserver.app directory and navigate to Contents>MacOS and type "cd GPserver.app/Contents/MacOS"
  3. Run the installer with "./GPserver"

We are continuting to work on updates to our documentation which reflect the latest version of GenePattern. That being said, let us know if you require clarification and let us know what you think by contacting us.

GenePattern server coverage & support Dec 24 - Jan 5

From December 24, 2014 to January 5, 2015, the GenePattern team will be out of office for the year-end closing of the Broad Institute. During this time, the GenePattern servers and repositories (including GParc) will remain up and fully functional. We will be monitoring this and, should anything happen to disrupt service, we will work to resolve any issues within 24 hrs. However, due to the holiday closing, please be aware that:

If you have any questions, please feel free to contact us.

 

Happy Holidays from the GenePattern team! 

 

 

GenePattern 3.9.0 Released

GenePattern 3.9.0 has been released!
3.9.0 is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:
  • A configurable disk usage quota
  • Job queue status indicator
  • Job status details, available on the job status page
  • Downloading of directories from the Files tab.
We also made some user requested fixes and enhancements:

Full details about 3.9.0, including hardware/software requirements and known issues can be found in our release notes.

Installing GenePattern on Mac OSX 10.9 (Mavericks) or 10.10 (Yosemite)
 
With Mac OS X 10.9 (Mavericks) Apple instituted a variety of application requirements that are incompatible with the GenePattern installer, which also apply to OS X 10.10 (Yosemite). As a consequence, those attempting to install GenePattern on Mavericks or Yosemite may encounter the following error message:

Despite this error message the GenePattern installer is not actually damaged. The message is part of a new Apple security measure. There are two options for working around this error and proceeding with a GenePattern installation, depending on your administrative privileges.
 
To determine if you have the appropriate admin privileges follow the instructions for "If you have admin privileges" below. If the “Allow apps downloaded from…” text remains grayed out throughout the steps, it is unlikely that you have the necessary privileges. In this case, please follow the steps beneath "If you do not have admin privileges."
 
If you have admin privileges:
 
If you are an admin on your Mac computer you can temporarily disable the security settings that prevent GenePattern from being installed. To do this perform the following steps:
  1. Open System Preferences (usually found in Applications > System Preferences)
  2. Click on the Security & Privacy icon
  3. Click on the General tab
  4. In the bottom half of the window make sure “Allow apps downloaded from…” is set to “Anywhere.” If this section is grayed out you may first have to click the lock icon in the lower left corner of the window and enter your password.
  5. Start the GenePattern installer by double-clicking the downloaded file. Once GenePattern is installed the previous security settings may be reapplied.
If you do not have admin privileges:
 
Another possibility for installing GenePattern is to start the installer from the command line. To do this perform the following steps:
  1. Using Terminal.app (found in Applications > Utilities), navigate to the Downloads directory.
    cd ~/Downloads
  2. Find the GPserver.app directory and navigate to Contents/MacOS
    cd GPserver.app/Contents/MacOS
  3. Run the installer:
    ./GPserver

This will start up the installer.

We are continuting to work on updates to our documentation which reflect the latest version of GenePattern. That being said, do let us know if you find anything to be out of date. We'll be happy to provide you with up-to-date information right away and update the page as soon as possible.

Please let us know what you think!

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