How to install XGAP locally

Step 1: Install and configure required software

XGAP is based on ​MOLGENIS which is known to run happily on Windows, Linux and Mac. We here assume the procedure for the windows installation; for other operating system distributions we refer to respective documentations. To get started, download and install the most recent:

• Java 6 JDK ​http://java.sun.com/javase/downloads/
  Just install the most recent standard JDK with standard options.
  
• Tomcat >=5 web server ​http://tomcat.apache.org/
  Remember the root password you are asked[[BR]]
• Mysql >=5.1 database ​http://dev.mysql.com/downloads/mysql/5.1.html [BR]]During installation of the windows version you need to tick 'innodb'. Remember your root password.
  
• Download XGAP .war and .sql files from ​sourceforge, current version xgap_1_2_distro

Step 2: Configure XGAP mysql database

Open mysql commandline client and:

• Create a database named 'xgap_1_2_distro'`

  create database xgap_1_2_distro;
  

• Allow molgenis (engine of XGAP) to read and write to this database as user 'molgenis'`

  grant all privileges on xgap_1_2_distro.* to 'molgenis'@'localhost' identified by 'molgenis'; 
  flush privileges;
  

• Select the database you just created.

  use xgap_1_2_distro;
  

• Copy-paste the contents of xgap_create_tables.sql in the mysql prompt to create the database. Alternatively, use command:

  source /path/to/xgap_create_tables.sql
  

Step 3: Run XGAP software on web server

• If not already started (as in windows) start Tomcat using the proper startup SH or BAT script

• Visit your local Tomcat Manager at
  http://localhost:8080/manager/html

• At "WAR file to deploy", select the XGAP_1_2_distro.war file and click "Deploy"

You can now use your XGAP at ​http://localhost:8080/xgap_1_2_distro/molgenis.do

Ideas for alternative distributions

Although quite straightforward, install of a local XGAP is still quite a hassle. Suggested alternative distributions include:

• XgapVmwareImage? -- create an VMware image that people can just run
• XgapInstaller? -- create installation script that does all above for you