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

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 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? 

  • From the Files Tab:
    • Delete files or directories
    • Save files or directories to a local drive
    • Save individual files to GenomeSpace, which can also provide the ability to save directly to DropboxAmazon Simple Storage System (S3) or Google Drive <pending release>, for short or long term storage. 



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: 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

Upcoming GenePattern Downtime

GenePattern downtime 7/25 - 7/28: Because of systems maintenance at the Broad, the following job queue interruptions will take place between 5 PM on Friday, July 25 and 10 AM Monday, July 28.


Please feel free to contact us if you have any questions or concerns

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