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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
  • 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

Linux

You can start and stop the CLC Bioinformatics Database service from the command line. You can also configure the service to start up automatically after the server machine is rebooted.

During installation of the CLC Bioinformatics Database a service script named CLCBioinformaticsDatabase is placed in /etc/init.d/ This script includes the name of the custom user account specified during installation for running the CLC Bioinformatics Database process.

Starting and stopped the service using the command line:

To start the CLC Bioinformatics Database:

sudo service CLCBioinformaticsDatabase start

To stop the CLC Bioinformatics Database:

sudo service CLCBioinformaticsDatabase stop

To restart the CLC Bioinformatics Database:

sudo service CLCBioinformaticsDatabase restart

To view the status of the CLC Bioinformatics Database:

sudo service CLCBioinformaticsDatabase status

Start service on boot up:

On Red Hat Enteprise Linux and SuSE this can be done using the command:

sudo chkconfig CLCBioinformaticsDatabase on

How to configure a service to automatically start on reboot depends on the specific Linux distribution. Please refer to your system documentation for further details.

Troubleshooting

If the CLC Bioinformatics Database is run as a service as suggested above, then the files in the installation area of the software and the data files created after installation in CLC Server File Locations will be owned by the user specified to run the CLC Bioinformatics Database process. If someone starts up the CLC Bioinformatics Database process as root (i.e. an account with super-user privileges) then the following steps are recommended to rectify the situation:

1. Stop the CLC Bioinformatics Database process using the script located within the installation area of the CLC Bioinformatics Database software. You can do that using the full path to this script, or by navigating to the installation area and running:

   sudo ./CLCBioinformaticsDatabase stop

2. Change ownership recursively on all files in the installation area of the software and on all areas specified as Server File Locations.

3. Start the CLC Bioinformatics Database service as the specified user by using the service script:

   sudo service CLCBioinformaticsDatabase start

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