Requirements

To install Galaxy, besides the Installation Package, you will need:

• A J2EE Servlet Container like Tomcat 5.0.x which is free or IBM WebSphere 5.1 which is a commercial product
• The Java 2 SDK Version 1.4.x from SUN's download pages, which is free
• a MySQL Database which is free
• The "production ready" MySQL JDBC Drivers which you can download freely from here.
• If you want to integrate Galaxy data into your Microsoft Office Documents, you can also grab the Microsoft Office XP Web Services Toolkit 2.0, which is also free

Unzip the Installation Package and you will have the following files:

File	Description
Galaxy.war	The war-file you have to deploy on your Application Server
createTables.sql	The script to create all the tables in the MySQL database
install_en.html	This file

Galaxy in the current Version relies on an MySQL database which you can download freely from their web site.

MySQL Version 4.1 Issue
Currently due to internal changes in MySQL Version 4.1, client software and libraries that access MySQL servers needs to be updated. This update is happening as of writing, but not yet complete. We therefore only support Galaxy to run with the previous 4.0 series of the MySQL Server.

Follow the documentation on the MySQL web site to install and configure the MySQL Database Server

TIP
If you have an Apache Web Server with PHP, then phpMyAdmin is a great software to work with MySQL databases. All this software is free.

Once you have the database installed and configured do the following:

1. Create a database that will be used by the Galaxy Server. For the sake of example we will call this database 'galaxyDatabase'
2. Create a database user that has access rights to this database. For the sake of example, we will call this user 'galaxyUser'
3. Ensure that galaxyUser has a password

1. Ensure that these two servers can actually "see" each other by a simple ping from each side
2. Ensure that the MySQL Server's permissions for galaxyUser allow her access from the server on which Galaxy will be running
3. Using the command like client, try to connect to the MySQL Server from the server on which Galaxy will be running, and make sure that you can connect

Once you have the database and the user created and ensured the user can access the database, its time to create tables in this database. To create the tables, you need to run the SQL commands that are in the createTables.sql file. You can do this either via the command line or some tool like phpMyAdmin. The command line would look something like:

$ mysql -u galaxyUser -pgalaxyUserPassword galaxyDatabase < createTables.sql

If the above command was successful, you should be able to login to the galaxyDatabase and execute the MySQL 'show tables' command that would list all the tables. You should also check that the Users table and the hibernate_unique_key table both have only 1 entry.

Upgrade Instructions: If you are updating the table model from Version 0.6 of Galaxy, please use the script 'update_V0_6_V1_0.sql' instead.

Once you have downloaded the JDBC package for MySQL, inside it you will find a file with the following name: mysql-connector-java-3.x.xx-ga-bin.jar. The 'x' will be different depending on which is the current version numbers.

Tomcat
Under Tomcat this can be achieved by dropping the jar file into the TOMCAT_INSTALL_DIR/common/lib directory and restarting the Tomcat Server.

If you want to use the Galaxy SQL connector to connect to a different type of database (like Oracle) you have to provide the JDBC connector for the particular database in the same way as the MySql JDBC connector.

The JDBC Driver classes for Oracle can be downloaded here.

With Tomcat copy this JDBC jar file into the TOMCAT_INSTALL_DIR/common/lib directory and then restart the Tomcat server.

WebSphere
With WebSphere, consult its documentation to setup a JDBC datasource, and follow the instructions and create a data source for MySQL and any other database that you wish to use.

This document contains instruction for deployment on two application servers: IBM's WebSphere 5.1 and Tomcat 5.0.x. At this stage, we will assume that you have installed the Application Server of your choice.

1. Login to the admin-application of WebSphere
2. In the menu choose Applications -> Enterprise applications
3. you will see a list of applications that are already installed
4. Choose install
5. Choose the location of the Galaxy.war on your local machine (you can use the browse button)
6. Specify the root-context of your application, please use the context /Galaxy for this version
7. During the install process you will be presented with a "Security Advise". You can ignore this advise and click on "Continue".
8. You have to walk through a list of 4 Steps to complete the installation. In this steps there is no configuration necessary, you just need to go through all of them.
9. After you have passed this steppes, the server will ask you to save the master configuration in order to activate the changes you made.
10. Applications -> Enterprise applications again, click on the new Installed Application to edit its properties
11. In the tab "Configuration" Change the "Mode of the Classloader" from "PARENT_FIRST" to "PARENT_LAST" and the "Policy for WAR-Classloader" from "Module" to "Application"
12. Choose "Apply" and Save the master-configuration
13. By default the new installed application is not started. To do so, you need to choose Applications -> Enterprise applications again, select the newly installed application and start it
14. After a while of processing, you should see a green icon indicating the started status for this application
15. The Galaxy application is now available on your server via the following URL http://[your.host]:[port]/Galaxy/wui
16. You will be directed to the Install page, this is described below

1. On the page that shows up after a fresh Tomcat install, click on "Tomcat Manager" and you will be asked to provide user name and password.
2. In case you don't have one, you will need to put an entry for a user in the tomcat-users.xml file in the conf directory of the Tomcat installation.
3. The entry should have a "manager" role. See Tomcat documentation about this for more details
4. Using the Tomcat Web Application Manager, in the Deploy section, you should "Select WAR file to upload",
5. Upload the supplied Galaxy.war file
6. Once uploaded, the application should be running, you can now go to the URL: http://[your.host]:[port]/Galaxy/wui to see the Install Pages which are described next.

The first time you start up Galaxy, you will be directed to the Install Pages. This is a 5 Step Process where you specify the MySQL database the Galaxy will connect to. Galaxy then check if it can really connect to this database and if everything is ok, then it starts the Galaxy Engine. The Steps are described below:

1. hostname: Hostname or IP address of your MySQL Server
2. port: the port of the MySQL Server (usually 3306)
3. username: the username to connect with
4. password: the password for this user
5. database: the database that contains all the tables for galaxy. In case you haven't created this database, a link to the SQL script is given on this step.

Step 2

In this step, the MySQL connection is tested, and if everything is ok, then you can proceed to Step 3

In this step, a check is made is the tables in the database that is provided in Step 1 match the ones that are needed. And if everything is ok, then proceed to step 4.

Step 5
In this step, click on the big Start Galaxy button. This is start up the Galaxy Engine and take you to the Login Page
Note Click this button only once!

Login Page
You can now login with the following data:

• Username: admin
• Password: galaxy

6. Next Steps

Ok, you have installed Galaxy, what now? The basic work cycle for Galaxy is as follows:

1. Create Connectors
2. Configure Requests for a Connector that have Input and/or Output Fields
3. Create Containers that use the Connector Fields
4. Do a "Sample Run" a Container to see if it works
5. Create Users and give them access to the Containers

For LDAP and SQL tutorials, go to: Galaxy Web site -> Documents -> Samples. Other tutorials will be put up there as well, so visit the Documents section regularly.

If you have any trouble installing, using or working with Galaxy, we encourage you to visit the Galaxy Forums and post your queries. Someone will definitely help you. Or if your prefer email, then email your queries at: galaxy[AT]sagadc[dot]com.

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