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

GenePattern 3.8.2

GenePattern 3.8.2 has been released! 3.8.2 (build 13519)  is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:

We also made some user requested fixes and enhancements:

Full details about 3.8.2, including hardware/software requirements and known issues can be found in our release notes.

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 That being said,  do let us know if you find anything to be out of date.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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