Table 9.11.1.

Required Parameters in the install conf File^a

Parameter	Description
TOMCAT_SERVER [nematoda.bio.nyu.edu]	Domain name of the Tomcat Web server. This will serve as the base URL for HTTP connections.
TOMCAT_PORT [8180]	Port number for Tomcat HTTP connections. The default port for Tomcat5 is 8180.
TOMCAT_WEBAPPS_PATH [/var/lib/tomcat5/webapps/]	Physical (directory) location of the Tomcat Web application in the file system. The default location for Tomcat5 is /var/lib/tomcat5/webapps/.
TOMCAT_APP_FOLDER [NBrowse]	Directory name to be used for the N-Browse Web application. If you plan to run multiple N-Browse servers on the same machine, this name can be customized to distinguish different instances.
MYSQL_SERVER [localhost]	MySQL server location for database connections. If the server resides on the same machine as the N-Browse server package, you can use “localhost.” If the database resides on a different machine, a domain name is required to make remote database connections.
MYSQL_PORT [3306]	MySQL server port number. You can leave it empty if you connect to “localhost” (MySQL default setting).
MYSQL_DATABASE_NAME [nbrowse]	Name of the MySQL database containing the N-Browse database schema (see Basic Protocol 4).
MYSQL_USERNAME [handler]	MySQL username that the N-Browse package will use as a handler for database connections.
MYSQL_PASSWORD []	MySQL password for the above MySQL user. It can be empty if the MySQL user has no password.
INSTALL_CYTOSCAPE_AUTOLAUNCH [Y/N]	Choose Y (yes) or N (no) to set up the Cytoscape auto-launch function. If Y, the next 3 parameters must be specified (JNLP_CODEBASE, JAVA_LOCATION, and CYJNLP_LOCATION).
JNLP_CODEBASE [nematoda.bio.nyu.edu/cgi-bin/nbTest/]	Web address (URL) for a directory on the N-Browse server machine in which Perl CGI scripts have permission to run (specified in Tomcat or Apache config files). This is essential to create the files for Cytoscape auto-launch.
JAVA_LOCATION[/usr/bin/]	Physical (directory) location of the JAVA binary.
CYJNLP_LOCATION [/usr/lib/cgi-bin/nbTest/]	Physical (directory) location of the Perl CGI scripts required for Cytoscape auto-launch.
WEBSITEHOSTBY [NYU Center for Genomics & Systems Biology]	Text for customizing the N-Browse Web site at your institution, to be displayed in an iFrame container at the top of the N-Browse Web pages at your site. If desired, you can further customize the Web site (with graphics etc.) by directly editing the HTML code in the containerInfo.html file included in the distribution.

^aThese parameters must be customized for your server machine prior to N-Browse installation. Example values for each parameter are provided in square brackets.