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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
- Licensing the CLC Server
  - Configuring and checking online licensing
  - Downloading a license
- Starting and stopping the server
Basic configuration
- Logging into the administrative interface
- Server display name
- Adding locations for saving data
- Changing the listening port
- SSL and encryption
- 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
- External network connections
- Proxy settings
Searching the web client
Managing users and groups
- Changing the root password
- User authentication for the CLC Server
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
Job processing
- 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 settings
Working with external data locations
- Import/export directories
- Direct data transfer from client systems
- AWS Connections in the CLC Server
- AWS S3 public buckets
- Browse AWS S3 locations
- Illumina BaseSpace
Working with CLC Server File System Locations
- Browsing CLC Server File System Locations
- Searching CLC Server File System Locations
Workflows
- Installing and configuring workflows
- Executing workflows
- Updating workflows
- Reference data in server workflows
BLAST databases
Status and management
- Server maintenance
- User statistics
- Server setup summary
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: Kraken2 (containerized external application)
  - Extending the Kraken2 external application for paired data
- 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
Recycle bins
- Automatic cleanup of recycle bins
- Emptying and restoring data from recycle bins
- Recycle bin restrictions
Configuring CLC Workbench connections
Troubleshooting
- Check setup
- Bug reporting
Command line tools
Analysis automation
Appendix
- Use of multi-core computers
- Non-exclusive Algorithms
- DRMAA libraries
- Consumable Resources
- Server system communication diagrams
  - Communication diagrams for CLC Servers using online licensing
  - Communication diagrams for CLC Servers using downloaded license files
- Third party libraries
- Read Mapper Reference Caching
- Controlling access to the CLC Server, data and execution environments
- Monitoring
Bibliography

Licensing

The CLC Server is a commercial product. A valid server license must be available before jobs can be submitted to a single server or master node to run on a CLC Server or another execution environment, such as a CLC Genomics Cloud setup^1.2.

An additional license is required for running tools delivered by commercial plugins ("server extensions").

The CLC Server web client and the CLC Server Command Line Tools do not require any additional license. To submit jobs from a CLC Workbench, that Workbench requires a valid license. Note that a licensed CLC Workbench is also required for designing and editing workflows, and for creating workflow installers.

When there is no valid license for the CLC Server, it runs in limited mode. In this mode, administrative users can log in to carry out configuration tasks, including making updates to licensing details.

Footnotes

... setup ^1.2: To run jobs on the cloud, the Cloud Server Plugin must be installed, an AWS Connection must be configured for an account with access to CLC Genomics Cloud infrastructure, and at least one cloud preset must be configured.