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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
- Server display name
- Adding locations for saving data
- Changing the listening port
- SSL and encryption
  - Logging in using SSL from a CLC Workbench
  - Logging in using SSL from the CLC Server Command Line Tools
- 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
Managing users and groups
- Changing the root password
- User authentication for the CLC Server
- 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 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
  - Rebuilding the index
Workflows
- Installing and configuring workflows
- Executing workflows
- Updating workflows
BLAST databases
Status and management
- Downloading a license via the web interface
- 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: 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 recycle bins
- Recycle bin restrictions
Configuring CLC Workbench connections
Troubleshooting
- Check setup
- Bug reporting
Command line tools
Appendix
- Use of multi-core computers
- Non-exclusive Algorithms
- DRMAA libraries
- Consumable Resources
- Server system communication diagrams
- Third party libraries
- Read Mapper Reference Caching
- Monitoring
Bibliography

Monitoring

We recommend that you monitor the health and performance of the servers that the CLC Server software is running on and also monitor some key metrics of the CLC Server itself. This will enable you to react quickly to any problems that occur and can aid in optimization of server performance.

With regards to the servers' physical resources, monitoring the amount of free memory and disk space is recommended, as consumption of these can be substantial depending on types and numbers of analyses being run.

Monitoring metrics of the CLC Server itself enables you to keep tabs on how well the jobs processing is going. The metrics the CLC Server provides are available as JMX^21.1 attributes. Software from a third party will be necessary to set up the monitoring of these attributes. Numerous software products for this are available and most support JMX. If your monitoring software supports the raising of alarms, you can set up triggers based on these metrics to receive alerts when a situation arises that needs attention.

Footnotes

... JMX ^21.1: https://en.wikipedia.org/wiki/Java_Management_Extensions

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