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• Introduction
  • System requirements
  • Licensing
  • Latest improvements
• Installation
  • Quick installation guide
  • Installing the database
    • Download and install a Database Management System
    • Create a new database and user/role
    • Initialize the database
  • Installing and running the Server
    • Installing the Server software
  • Installation modes - console and silent
  • Upgrading an existing installation
    • Upgrading major versions
  • Allowing access through your firewall
  • Downloading a license
    • Windows license download
    • Mac OS license download
    • Linux license download
    • Download a static license on a non-networked machine
  • Starting and stopping the server
    • Microsoft Windows
    • Mac OS X
    • Linux
  • Installing relevant plugins in the Workbench
• Configuration
  • Logging into the administrative interface
  • Adding locations for saving data
    • Adding a file system location
    • Adding a database location
    • Rebuilding the index
  • Changing the listening port
  • Setting the amount of memory available for the JVM
  • HTTP settings
  • Deployment of server information to CLC Workbenches
• Managing users and groups
  • Logging in the first time and changing the root password
  • User authentication using the web interface
    • Authentication options
    • Managing users using the web interface
    • Managing groups using the web interface
  • User authentication using the Workbench
    • Managing users through the Workbench
    • Managing groups through the Workbench
    • Adding users to a group
• Access privileges and permissions
  • Controlling access to CLC Server data
    • Setting permissions on a folder
    • Recycle bin
    • Technical notes about permissions and security
• Queue
• Status and management
  • User statistics
  • System statistics
  • Server maintenance
• Audit log
  • Customized attributes on data locations
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
    • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
• Appendix
  • Troubleshooting
    • Check set-up
    • Bug reporting
  • Database configurations
    • Getting and installing JDBC drivers
    • Configurations for MySQL
  • SSL and encryption
    • Enabling SSL on the server
    • Logging in using SSL from the Workbench
    • Logging in using SSL from the CLC Server Command Line Tools
  • Third party libraries
• Bibliography

Download and install a Database Management System

If you do not already have an existing installation of a Database Management System (DBMS) you will have to download and install one. CLC Bioinformatics Database can be used with a number of different DMBS implementations. Choosing the right one for you and your organization depends on many factors such as price, performance, scalability, security, platform-support, etc.

Information about the supported solutions are available on the links below.

• MySQL: http://dev.mysql.com/downloads/
• PostgreSQL: http://www.postgresql.org/
• Microsoft SQL Server: http://www.microsoft.com/SQL/
• Oracle: http://www.oracle.com/

In the case of MySQL and Oracle, you will need to have the appropriate JDBC driver and this will need to be placed in the userlib folder of the CLC software installation area. See Database configurations for further details on this as well as additional guidance for special configurations for DBMSs.

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