To make BioCoRE run on your own system, we are basically going to follow the instructions at:

for installing a local server, with the main exception being that you aren't going to use precompiled binaries. You are going from source. So, you need to follow the local server installation instructions down to the step where you test tomcat and install the BioCoRE files. Do NOT install them from the WAR file. You will compile them yourself.

Getting BioCoRE installed for the first time when using source code:

  1. For compiling BioCoRE, you need to be using Java 1.4. Although Java 1.5 is available, there are several compatibility issues that make it unsuitable for BioCoRE. In particular, if you use Java 1.5 to compile the BioCoRE web start applications (such as the Control Panel) all of your users will be forced to use Java 1.5 to access them. It's much nicer to not require the users to upgrade if they don't need to. So, we use Java 1.4 for compilation on our system and will continue for the foreseeable future, until we are confident that the large majority of users are running Java 1.5 or higher.
  2. To compile, you need to have Apache Jakarta's 'ant' build tool.

    You can download this from:

    We suggest that you install it in the packages directory described in the above localServer URL and sym link 'current' just like you have done with the other packages. We have been using ant version 1.6.2, but any newer version should work (you do need at least 1.5). We also suggest that you add the ant bin directory to your path.

    Once you have done this, you need to copy a jar file from the Tomcat directory to your ant directory. Assuming you installed Tomcat in the location described in the normal installation instructions you need to copy the file $BIOCORE_HOME/packages/tomcat/current/server/lib/catalina-ant.jar into the lib/ subdirectory where you installed ant. The lib/ subdirectory should have been created when you uncompressed the ant tarball.

  3. Environment variable settings: You need to have the following set in your environment. We suggest that you put in them in your init scripts so that you don't have to remember to set them each time you login:

    • Make sure that your path contains java and ant bin directories.

    • ANT_HOME needs to be set to the ant directory.

    • JAVA_HOME needs to be set to the java directory.

    • BIOCORE_PATH needs to be set to the $BIOCORE_HOME directory discussed in the server install documentation.
  4. You need to edit $BIOCORE_HOME/packages/tomcat/current/conf/tomcat-users.xml and add a line that looks like:
  5. Uncompress the source file tarball. A directory called biocore will be created.
  6. Create Place the following lines in a file called '' in the top level biocore directory (the same directory that contains build.xml). Modify to point to your own copy of tomcat and set the other entries appropriately Be very careful to make sure that there are not any spaces/blank characters at the end of each line. This has been known to cause problems.
    # ----------------------------------------------
    # destination path for my copy of tomcat
    # location of netscape jar files
    #  Because signed applets are being used, we have to have netscape's
    #  signing classes.  Find the java40.jar file on your system and point
    #  this variable to it.
    # base location where we can find necessary external 
    # Globus jar files build.xml references files in
    #    ${biocore.base}/globus/gpdk/lib/
    # IF you don't have Globus installed, just leave this with the
    # default value and everything will still work, without Globus
    # support.
    # location of swing as well as the java 1.1.x class files.  This is
    # needed so that applets know which APIs they can actually use and
    # still expect to work in current browsers.
    # used for jar signing.  If you have a real certificate, uncomment
    # and modify the following
    #signAlias=Exact Alias Name That You have verisign, inc. id
    # path to the mysql connector.  If this is commented out, version 2.0.14 of 
    # the connector is used.  If you are using mysql  4.1+ you must use a
    # different connector, though.  Only uncomment if needed.
    # ----------------------------------------------
    url needs to point to the machine that tomcat is on. username, password need to match the values you put into the tomcat-users.xml file earlier.
  7. From the biocore directory, compile and deploy the binaries to Tomcat by saying:
      ant deploy
You are now ready to continue on with the installation instructions for a local server. Finish those steps up and you should have a working BioCoRE server.

Once you have a working server and want to modify BioCoRE code, please refer to the section on working with the source code.


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.