GenePattern Team Blog

Workarounds to Install and Run a GenePattern Server on Mac OS X 10.9 Mavericks

Posted on Wednesday, May 07, 2014 at 05:49PM by David Eby

In a previous blog post we gave some limited instructions for using GenePattern with Mac OS X 10.9 Mavericks.  While accessing the public server via web browser is not an issue, installing and running your own GenePattern server is a different matter.  Issues with the installer, server launcher, and general responsiveness prevent us from officially supporting this platform right now.  We are actively working to address these problems and expect to have a fix in a future version of GenePattern, as soon as is feasibly possible.  This is very important to us and is on our immediate agenda.

In the meanwhile, however, we have some new workaround recommendations which should improve your current experience running the GenePattern server on Mavericks.

I'll start off by explaining how to launch GenePattern server for the benefit of those folks who had it installed and working on an earlier version of OS X but then upgraded to Mavericks and ran into the responsiveness...

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GenePattern 3.8.1

Posted on Thursday, April 17, 2014 at 05:29PM by GenePattern Team

GenePattern 3.8.1 has been released! 3.8.1 (build 13243)  is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:

  • A new file uploader, replacing the Java-Applet-based file uploader with a new html5/JavaScript file uploader
  • New Jobs and Files tabs, which introduce new slide-out menus for all jobs and job output files
  • The ability to group parameters; for instance into "Advanced" and "Basic"
  • Website tours which walk users through new and basic features of GenePattern

We also made some user requested fixes and enhancements:

  • The new file uploader eliminates file upload failures occasionally encountered when uploading large files using the retired applet-based uploader.
  • Previously there existed a bug which prevented the termination of pending jobs. This has been resolved.

Full details about 3.8.1, including hardware/software requirements and known issues...

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GenePattern 3.8.0

Posted on Wednesday, February 12, 2014 at 04:42PM by GenePattern Team

GenePattern 3.8.0 has been released! 

3.8.0 (build 12839)  is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:

  • An updated User Interface
  • New and improved Modules & Pipelines Pane
  • Pinning favorite modules
  • Running a batch job over multiple dragged in files
  • Parallel execution of jobs in a pipeline
  • Pipeline designer improvements allowing the use of regular expressions to specify output files to be used as downstream input.
  • Multiple categories for individual modules and pipelines
  • Directories in dynamic drop downs
  • Setting of file purge intervals based on user or group

We also made some user requested fixes and enhancements:

  • A bug in GenePattern's SGE integration prevented job cancelation. This has been resolved.
  • Previously the pipeline designer did not allow non-admin users with createPublicPipeline permission to create public pipelines. This has been...

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