Note: If you are updating from the old version of the server (prior to July of 2005) to the newly redesigned and released server (August 2005 or later), please visit our update page made specifically for that purpose.

This page assumes that you already have a local BioCoRE server installed and you just need to update the BioCoRE code. Furthermore, these instructions assume that you have followed the BioCoRE server installation instructions when installing your server with regard to paths, locations of files within those paths, etc. Note that while you have tomcat shutdown that the BioCoRE collaboratory will be inaccessible by users.

Steps Involved

  1. Download Updated BioCoRE Files- From the download database, download the newest version of the BioCoRE server software.
  2. Unpack the downloaded tarball into a temporary directory.
  3. Review the README file to see if it contains any information not discussed here. This is a very important step because, from time to time, you might need to perform a step not discussed here because these are general upgrade instructions.
  4. Shutdown tomcat- Change to the $BIOCORE_HOME/packages/tomcat/current/bin directory and run ./
  5. Change to the $BIOCORE_HOME/packages/tomcat/current/webapps directory and delete the biocore directory. If you had changed any files in that directory be sure to copy the changed files to a safe location before deleting the directory.
  6. Create a new subdirectory called biocore. Change to the new directory you just created, and unpack the biocore.war file:

    $BIOCORE_HOME/java/current/bin/jar xvf /PATH/TO/biocore.war
    This will uncompress the WAR file.
  7. Run the script that came in your tar file that you downloaded. It will tell you that Globus support isn't activated, and you can ignore that for now. It should tell you that it is done and you can now start tomcat. (Note: this install script depends on the .biocoreInstallrc file that you created in your home directory when you originally installed BioCoRE. You might wish to review the values in the file and make sure they are correct before running
  8. Restart tomcat by running ./ from the bin directory.


The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.