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!

Change in GenePattern Data Storage Policy

Changes to the GenePattern Storage Policy
On October 6, 2014, we will be making some changes to the way that data is stored for your account on genepattern.broadinstitute.org:

We will send you messages in advance of the dates if you will be affected by either of these policies. Please feel free to contact us at gp-help@broadinstitute.org if you have any extenuating circumstances, questions, or concerns.
 
Additional information
 
What data is subject to the quota? Quotas apply only to files stored in the Files Tab and do not apply to job results, which remain on the server for 7 days.

How can I tell how close I am to my quota? Your quota usage will be visible in the upper right hand corner of the UI

 

What will happen when I am near my quota? 

  • When near or exceeding the 30GB limit, the bar will become red

 

  • If you try to add a file that exceeds the quota, you will see an error message indicating that the file will not be added, and will provide suggestions on how to remove files from your Files Tab.

 

  • If you try to run a new job after your quota has been exceeded, you will also see the above error, and you will not be able to run new jobs until this has been resolved. 

How can I remove data from my account? 

 

 

Please be in touch if you have any questions or comments.

Changes to Startup Env Impact R Modules on Broad Hosted Servers

Changes to Startup Env Impact R Modules on Broad Hosted Servers: As a result of the software update on August 14, we modified the startup environment for the server. This was necessary because the server now requires Java 7. It was previously using Java 6. Surprisingly, this necessitated a change to the R configuration. You may notice slight changes to the behavior of your R modules. For example, the ATLANTISInputs module failed with this error message:

	/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

The workaround is to change the command line for your R modules to use the preferred command line substitution parameter. For example, for an R 3.0 module use <R3.0_Rscript>. For an R 2.15 module use <R2.15_Rscript>. Please contact us for further assistance. Thanks! Originally posted on gpbroad at 4pm on Monday Aug 25

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