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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
    • Microsoft Windows
    • macOS
    • Linux
• Basic configuration
  • Logging into the administrative interface
  • Server display name
  • Adding locations for saving data
    • CLC Server File System Locations
    • Reference data management
    • Enabling and disabling internal compression of CLC 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
    • Giving users administration rights
    • 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
    • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching custom attributes
• Job processing
  • Introduction to servers setups
  • Model I: Master server with dedicated job nodes
    • Overview: Model I
    • User credentials on a master-job node setup
    • Configuring your setup
    • Installing Server plugins on job nodes
  • Model II: Master server submitting to grid nodes
    • Overview: Model II
    • Requirements for CLC Grid Integration
    • Technical overview
    • Setting up the grid integration
    • Configuring the master node for a grid setup
    • Licensing of grid workers
    • Configuring licenses as a consumable resource
    • Configuring grid presets
    • Controlling the number of cores utilized
    • Multi-job processing on grid
    • Other grid worker options
    • Testing a Grid Preset
    • Client-side: submitting CLC jobs to the grid
    • Grid Integration Tips
    • Understanding memory settings
  • Model III: Single Server setup
  • Workflow settings
    • Workflow distribution options
    • Choosing a workflow distribution option
    • Intermediate workflow result handling
• 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
    • Editing external applications
    • External command
    • High-throughput sequencing import / Post-processing
    • Stream handling
    • Failure strategy
    • Environment
    • End user interface
    • Management
  • Using consistent reference data in external applications
  • Import and export of external application configurations
  • Updating external application configurations
  • Example: Velvet (standard external application)
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • Example: Bowtie (standard external application)
    • Installing Bowtie
    • Understanding the Bowtie Map configuration
    • Setting the path for temporary data
    • Tools for building index files
  • 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
    • DRMAA for SLURM
    • DRMAA for LSF
    • DRMAA for PBS Pro
    • DRMAA for OGE or SGE
  • Consumable Resources
  • Server system communication diagrams
  • Third party libraries
  • Read Mapper Reference Caching
  • Monitoring
    • Setting up JMX monitoring
    • Completed process metrics
    • Process execution metrics
    • Job node metrics
• Bibliography

Upgrading between major versions

There are a few extra steps needed when upgrading to a new major version line beyond those outlined in Upgrading an existing installation.

1. Download a license file valid for the new major version on a single server, or on the master server in a job node or grid node setup, if this has not already been done. See Downloading a license.

2. Delete old license files. License files can be found in a folder called "licenses" under the installation area of the CLC Server.
3. Restart the CLC Server service. See Starting and stopping the server.
4. All users of client software (CLC Workbenches and the CLC Server Command Line Tools) must upgrade their software. Corresponding and compatible software versions are listed at the bottom of the Latest Improvement listings for a given server version. e.g. for the latest release, this can be found at: https://digitalinsights.qiagen.com/products/qiagen-clc-genomics-server/latest-improvements/current-line/.

• All plugins installed on the CLC Server need to be updated. See Server plugins.

• On job nodes, any new tools included in the server upgrade will need to be enabled for the nodes you wish them to be run on. New tools are initially disabled on all job nodes to avoid interfering with a setup where certain nodes are dedicated to running specific types of jobs. Read more about enabling tools on job nodes in Configuring your setup.

Configuration updates required when upgrading to CLC Genomics Server 22.0 or higher

If you have configured custom listening port or SSL settings, these need to be reconfigured after upgrading to CLC Server 22.0 and above from older release lines (21.x and earlier), due to an update to Tomcat.

• Configuring a custom listening port is described in Changing the listening port.
• Enabling SSL is described in Enabling SSL on the server.

When upgrading, a backup of your previous configuration will have been saved to conf/server.xml.backup, under the installation area. This file can be referred to for information relevant for configuring the new conf/server.xml file.

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