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Introduction
- System requirements
- Licensing
- CLC Genomics Server
Installation
- Quick installation guide
- Installing and running the Server
  - Installing the Server software
- Installation modes - console and silent
- Upgrading an existing installation
  - Upgrading between major versions
- Allowing access through your firewall
- Downloading a license
  - Download a static license on a non-networked machine
- Starting and stopping the server
Basic configuration
- Logging into the administrative interface
- Adding locations for saving data
- Changing the listening port
- Changing the tmp directory
  - Job node setup
- Setting the amount of memory available for the JVM
- Limiting the number of cpus available for use
- 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 and groups using built-in authentication
- User authentication via the Workbench for built-in authentication
Access privileges and permissions
- Controlling group access to CLC Server data
  - Setting permissions on folders
  - Technical notes about permissions and security
- Controlling access to the server, server tasks and external data
- Customized attributes on data locations
Job distribution
- Introduction to servers setups
- Model I: Master server with dedicated job nodes
- Model II: Master server submitting to grid nodes
- Model III: Single Server setup
- Workflow queuing options
  - Choosing a workflow queuing option
- Job running options
Access to files outside CLC Server Locations
- Import/export directories
- Direct data transfer from client systems
- AWS Connections
- Illumina BaseSpace
Workflows
- Installing and configuring workflows
- Executing workflows
- Updating workflows
BLAST databases
- Adding directories for BLAST databases on the Server
- Adding and removing BLAST databases
Status and management
- Downloading a license via the web interface
  - Download a static license on a non-networked machine
- Server maintenance
- User statistics
- System statistics
Queue
Audit log
Server plugins
External applications
- External application configurations
  - Configuring the containerized execution environment
- Configuring external applications
- Using consistent reference data in external applications
- Import and export of external application configurations
- Updating external application configurations
- Example: Velvet (standard external application)
- Example: Bowtie (standard external application)
- Example: MAFFT (containerized external application)
- External applications in workflows
- Running external applications
  - Using a CLC Workbench to launch external applications
  - Using CLC Server Command Line Tools to launch external applications
- Troubleshooting external applications
CLC Genomics Cloud Access
Browsing and searching for data
- Browsing CLC Server data locations
- Searching CLC Server data locations
  - Rebuilding the index
- Browse a CLC Server import/export directory
- Browse AWS S3 locations
Recycle bins
Troubleshooting
- Check setup
- Bug reporting
Command line tools
Appendix
- Use of multi-core computers
- SSL and encryption
- Non-exclusive Algorithms
- DRMAA libraries
- Consumable Resources
- Third party libraries
- External network connections
  - Proxy settings
- Read Mapper Reference Caching
- Monitoring
Bibliography

Changing the listening port

The default listening port for the CLC Server is 7777. This has been chosen to minimize the risk of collisions with existing web-servers using the more familiar ports 80 and 8080. To have the server listen on a different port:

Navigate to the CLC Server installation directory.
Locate the file called server.xml in the conf directory.

Open the file in a text editor and locate the following section

	    <Connector port="7777" protocol="HTTP/1.1" 
	    connectionTimeout="600000" compression="off" />

Change the port value to desired listening port (8080 in the example below)

	    <Connector port="8080" protocol="HTTP/1.1" 
		connectionTimeout="600000" compression="off" />

Restart the service for the changes to take effect. See Starting and stopping the server).
After restarting, log into the web administrative interface and change the default port number in the "Master node port" field under Configuration | Job distribution | Server setup, and then click on Save Configuration button to save the new setting.