GenePattern 1.0.0 Release Notes

Released March 1, 2004

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 a single computer has multiple instances of GenePattern running, they must not be allowed to share a single HSQL instance. Doing so would cause some jobs to be run multiple times, and job results would be randomly retrievable from one server or the other. HSQL will quietly die if started a second time on the same port, but the clients that connect to a single instance will all be "happy", though not for long.

  • Tomcat listens on some ports other than 8080 (for purposes other than listening for web browsers), and having multiple Tomcat server instances on a single machine (whether GenePattern or not) will require that they be assigned unique port numbers per instance. Shutdown port=8005.

  • Pre-installed tasks have their documentation in Adobe Acrobat PDF file format. You will need to have the free Acrobat Reader installed on your computer in order to view this documentation. It can be downloaded from

  • 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 privilege), you can have it 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 from your installation.

  • Under Linux, the installer will not automatically start the GenePattern server when it is done.

  • Under Mac OS X, you must have write permission for the /Applications folder in order to install R.

  • If you install the server on a non-default Tomcat port (not 8080), the GenePattern Client installer will not automatically select this port for you to connect to. You must change it manually during installation.

  • When re-installing, you must shutdown the existing, running server first.

Pipeline issues:

  • When you try to upload a task zip file, if the zip file contains a directory hierarchy and does not have all files in a flat structure,when you upload you get an error stating that a directory is unwritable.

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

  • If you edit the pipeline R code and later regenerate the pipeline using the pipeline designer, your code changes will be overwritten without warning.

  • Your GenePattern username is used as the sender email address for pipeline results. Some SMTP mail servers require that this be a valid, local email address. Using simply a username without "" may not work. If it fails you will see a pop-up browser window allowing you to edit the sender address when a pipeline completes and notification was requested.

  • If you rename a task, pipelines that refer to the old task name are not updated to reflect the new name. Similarly, if you rename or delete parameters from a task, pipelines that refer to that task are not updated and will fail.

  • Pipeline input files with spaces in their names may give file-not-found errors. If this happens, use DOS' "dir /x" command to get the 8.3 version of the directory and filename and use that instead of the long filename. If you are using a Unix-based platform, you may need to quote the filename parameters on the command line definition.

  • Pipelines created with input prompts may not run on the client and also could have wrong UI input (input field instead of a drop down menu).

  • If you edit the R pipeline code and have an error in your code, the error message reported will be Error: syntax error, execution halted. No mention is made of the line on which the error occurs.

  • The pipeline designer functions best when browser page caching is disabled. In Netscape Navigator 7.0 and 7.1, go to Edit->Preferences->Advanced->Cache, set the cache size to zero and clear the cache.

  • You may have problems sharing published pipelines with other users if you override the default Tomcat port number (8080) during installation.

  • Zipping a pipeline for sharing does not recursively zip the associated tasks used by the pipeline. Zip them separately if you need to.

Graphical client issues:

  • The File system view does not show drive roots (ie. other drive letters) under Windows.

Task creation, execution, and sharing issues:

  • GenePattern does not distinguish between two users with same-named tasks. If one user creates a task with the same name as an existing one owned by a different user, it will overwrite it.

  • The following input filenames will not work, regardless of the extension they are given, on servers running on Windows machines: con, prn, aux, clock$, nul, com, com1, com2, com3, com4, lpt1, lpt2, lpt3.

  • CPU- and OS-restrictions on task execution are not currently enforced, and there is no warning if the restrictions are violated.

Module-specific issues: