• Manuals

Browse the manual

• 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
  • Silent installation
  • 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
  • Starting and stopping the server
    • Microsoft Windows
    • Mac OS X
    • Linux
  • Installing relevant plugins in the Workbench
• Configuring and administering the server
  • Logging into the administrative interface
  • Adding locations for saving data
    • Adding a database location
    • Adding a file system location
    • Rebuilding the index
  • Changing the listening port
  • Setting the amount of memory available for the JVM
  • Limiting the number of cpus available for use
  • Other configurations
    • HTTP settings
    • Audit log settings
    • Deployment of server information to CLC Workbenches
• Managing users and groups
  • Logging in the first time and the root password
  • User authentication using the web interface
    • 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
  • User statistics
• Access privileges and permissions
  • Controlling access to data
    • Setting permissions on a folder
    • Recycle bin
    • Technical notes about permissions and security
  • Global permissions
  • 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 the sequence 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

Quick installation guide

The following describes briefly the steps needed to set up a CLC Bioinformatics Database 4.0 with pointers to more detailed explanation of each step.

1. Download and run the server installer. As part of the installation, choose to start the server (more).
2. Run the license download script that is part of the installation (more).
3. The script will automatically download a license file and place it in the server installation directory under licenses.
4. Restart the server (more).
5. Log into the server using a web browser (note that the default port is 7777) with username root and password default (more).
6. Change the root password (more).
7. Configure authentication mechanism and optionally set up users and groups (more).
8. Add data locations (more).
9. Download and install plug-ins in the Workbench needed for the Workbench to contact the server (more).
10. Check your server set-up using the Check set-up tool.
11. Your server is now ready for use.

---