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 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:
Open System Preferences (usually found in Applications > System Preferences)
Click on the Security & Privacy icon
Click on the General tab
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.
Start the GenePattern installer by double-clicking the downloaded file. Once GenePattern is installed the previous security settings may be reapplied.
Another possibility for installing GenePattern is to start the installer from the command line. To do this perform the following steps:
Using Terminal.app (found in Applications > Utilities), navigate to the Downloads directory. cd ~/Downloads
Find the GPserver.app directory and navigate to Contents/MacOS cd GPserver.app/Contents/MacOS
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 That being said, do let us know if you find anything to be out of date.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.
Posted by Barbara Hill Meyers on Monday, September 22, 2014 at 03:26PM
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:
Your account will have a storage quota of 30GB. To accommodate the increased use of the Broad's GenePattern server, each user account will have 30GB to store files in the Files tab.
Data in inactive accounts will be removed. If you haven't logged into your GenePattern account in the past 6 months, we will clear the data that is associated with your account.
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 firstname.lastname@example.org you have any extenuating circumstances, questions, or concerns.
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.
Posted by Peter Carr on Thursday, September 18, 2014 at 04:52PM
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