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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

Server system communication diagrams

The communication between CLC software and other local resources for some common CLC Server setups are summarized in the diagrams provided in this section.

These diagrams do not include representation of communication with external resources, such as accessing reference data from remote locations, downloading licenses for CLC software, or interacting with a CLC Genomics Cloud setup.

Communication diagrams for CLC Servers using online licensing:

Grid setup with LDAP authentication: figure 23.1
Grid setup with built-in authentication: figure 23.2
Job node setup with LDAP authentication: figure 23.3
Job node setup with built-in authentication: figure 23.4

Communication diagrams for CLC Servers using downloaded license files:

Grid setup with LDAP authentication: figure 23.5
Grid setup with built-in authentication: figure 23.6
Job node setup with LDAP authentication: figure 23.7
Job node setup with built-in authentication: figure 23.8

Subsections