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1. Unix-like operating system. This procedure is only valid for Unix variants like Linux, Solaris, MacOSX. To run some of the scripts you will need to have these commands installed:
   • bash
   • perl
   • curl
   • awk (surely anything that calls itself unix must have awk)
   • tr (seriously, is tr missing? if you are running Gentoo, install an operating system)
2. Sun's Java JDK 1.6.0.18 (though any 1.6 version ought to work just as well).
3. Apache Tomcat web servlet container, version 6.0 or 7.0 (version 7.0 should work but we haven't thoroughly tested; this guide refers to version 6.0), configured to run with the Java JDK in #2.
   • Make sure you follow Tomcat installation and configuration instructions for the Tomcat version and Linux distribution you are using; before installing the eagle-i repository, Tomcat must be fully functional. You may want to test this by using Tomcat's manager app, which should be available at http://localhost/manager/html/ - you will need to edit the file conf/tomcat-users.xml for defining a user and a role - see this guide: Apache Tomcat 6.0 Manager App HOW_TO
   • Tomcat must be configured to use SSL, see for examplethe quickstart section here: Apache Tomcat 6.0 SSL Configuration HOW-TO
   • See the Procedures section if using Ubuntu's tomcat6 package.
   • It may be necessary to download Tomcat directly and install it manually if the version supplied by the host OS's package system is not usable. Don't hesitate to do this if it is expedient; Tomcat can run as a pure Java application in a single file hierarchy, so a manual download can work just as well (if not better) than the packaged version.
4. Optional: Apache Derby RDBMS installed in your Tomcat servlet container.
   • A copy of Derby is provided if you need to install it.

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Ensure that your Tomcat server is run with the following options on its JVM. The simplest way to accomplish this is to have the environment variable JAVA_OPTS include those options, but each platform, distro, package etc. of Tomcat has its own mechanism for setting this variable. For example, on Fedora 14, it should be in the file /etc/tomcat6/tomcat6.conf.Here is an exampleetc. of Tomcat has its own mechanism for setting this variable. For example, on Fedora 14, it should be in the file /etc/tomcat6/tomcat6.conf. If you can't find your distribution's configuration file, you may create a file setenv.sh in tomcat's bin directory to add the environment variable:

...(ONLY DO THIS if you can't find your distribution's config file)
cd ${CATALINA_HOME}/bin
touch setenv.sh

Edit the configuration file (tomcat6.conf, setenv.sh or whatever your distribution uses) and add the following line:

JAVA_OPTS="-XX:PermSize=64M -XX:MaxPermSize=256M -Xmx1024m"

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Follow this step-by-step procedure. Before you start, make sure the Tomcat server is not running.

1. Navigate to Tomcat's webapps directory. If there exist a directory named ROOT, move it aside. The eagle-i repository must be the ROOT application

   Code Block
   cd ${CATALINA_HOME}/webapps mv ROOT ROOT.original

2. Copy the webapps to the Tomcat webapps directory:

   Code Block
   cp ${REPO_HOME}/webapps/* ${CATALINA_HOME}/webapps

3. Create your be initial administrative user login. Think of a USERNAME and PASSWORD and substitute them for the italicized words in this command:

   Code Block
   bash ${REPO_HOME}/etc/prepare-install.sh USERNAME PASSWORD ${REPO_HOME}

4. Start up the servlet container (Tomcat).
5. Run the finish-install script, which loads the data model ontology among other things. Note that you can also give it additional options to specify a personal name and email box for the initial admin user. 

   Code Block
   bash ${REPO_HOME}/etc/finish-install.sh USERNAME PASSWORD https://localhost:8443

   ...or, with username metadata included:

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