GenePattern 1.2.1 Release Notes

Released November 1, 2004

The 1.2.1 release fixes the following issues:

  • The Data Object Browser parses XML file types correctly.
  • On MS Internet Explorer, the Task Installer can now install an unlimited number of tasks from the Broad Institute module repository in a single request.
  • Visualizers with a missing optional file input parameter, such as HierarchicalClusteringViewer, can now be launched

New in release 1.2:


  • Visualizers can be written in any language. In addition to Java, visualizers can be written in any language that is supported by the client's operating system.


  • Module installation and update over the web. Instead of containing a pre-set list of modules, the GenePattern installation now allows users to choose from any of the most up-to-date modules available at the GenePattern public website. There is a link to the catalog from the GenePattern home page on your server.


  • Java Programming Language Environment. In addition to the R language, you can now convert pipelines to Java code and incorporate calls to GenePattern modules from a Java application.


  • Pipelines can include visualizers. A visualizer can be used as any step in a pipeline.
  • Automatic output file names. File name templates can be specified for all result files, so you do not have to type the name of each output file in an analysis or pipeline.


  • Graphical Client Enhancements. In the GenePattern Graphical Client, you can refresh the list of available modules without restarting the client. The client will also automatically relaunch when you change the server to which it is connected.


Other new features:


  • The graphical client has been simplified by removing the infrequently used "Data Objects" and "File View" tabs.
  • Launch any GenePattern visualizer from an R or Java program.
  • Improved display functionality in Web client


Installation and system configuration issues:


  • If your browser is configured to block popups, you won't be able to email pipeline results, stop running pipelines, or see various pipeline error messages displayed. In Netscape Navigator 7.1, this is controlled via Edit->Preferences->Privacy & Security->Popup Windows.


  • If you are using a version of R which you cannot modify (because it is a publicly-shared version and you don't have appropriate privileges), you can load the GenePattern library by setting the environment variable R_LIBS=<GenePattern install directory>/R/library in your autoexec.bat, .cshrc, .bashrc or other shell startup file. R will then load from its usual location, but will also search for and find the GenePattern library.


Linux Issues

  • Under Linux, if you do not have write permissions into the R installation directories your install will complete but will note some errors during installation. The server will be unable to execute pipelines unless you reinstall the GenePattern server with the appropriate privileges or follow the directions (above) for using a version of R which you cannot modify.
  • To install under Mandrake Linux 9.2, you must install the binutils, libstdc++, gcc, and libxml packages. Use rpmdrake to search for and install them.

Pipeline issues:


  • If you created any pipelines under previous versions of GenePattern, you will get an error when you attempt to run them in GenePattern 1.2. Open and save them in the pipeline designer and these pipelines will work correctly.


  • "Prompt when run" for pipeline parameter selections to be made at pipeline execution time, does not work for pipelines run in the Web client, only for those run from the Java or R clients.


  • If you rename a task, you must manually update pipelines that refer to that task. Similarly, if you rename or delete parameters of a task, you must change the parameters in pipelines that refer to that task.


Graphical client issues:


  • When errors or other messages appear, their windows may be hidden underneath another window. If you click in the client window and get no response, you may need to switch (Windows Alt-Tab, Mac Cmd-Tab) to that window and close it.


  • Input files may not include spaces.


  • The HTML file viewer on Linux is hardwired to "netscape". If you want to view HTML files in a different browser, you can create a soft link from your browser to netscape (e.g. ln -s /usr/bin/mozilla /usr/bin/netscape)


Task creation, execution, and sharing issues:


  • If, when you save a task for the first time, you are asked if you want to overwrite that task, it means that another user has created a task with the same name. If you save the task, it will overwrite the previous one.

Module-specific issues:



  • SVM: Confidence values are not computed and are set to the value 1.


  • Perl modules will produce incorrect output if input files contain line endings that are different from the host operating system's line endings. For example, submitting a file with Windows line endings to SplitDatasetTrainTest on a Linux GenePattern server will produce incorrect results. Use the ConvertLineEndings task to make the conversion, if necessary.

Programming language environment issues:



  • R scripts cannot read binary result files.