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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
  • Installing the database
    • Download and install a Database Management System
    • Create a new database and user/role
    • Initialize the database
• Basic configuration
  • Logging into the administrative interface
  • Adding locations for saving data
    • File system locations
    • Reference data management
    • Enabling and disabling internal compression of CLC data
    • Database locations
    • Rebuilding the index
  • Accessing files on, and writing to, areas of the server filesystem
  • Direct data transfer from client systems
  • 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 using the Workbench
    • Managing users through the Workbench
    • Managing groups through the Workbench
• Access privileges and permissions
  • Controlling access to CLC Server data
    • Setting permissions on a folder
    • Recycle bin
    • 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
• Job distribution
  • 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
    • Licensing of grid workers
    • Configuring licenses as a consumable resource
    • Configure grid presets
    • Controlling the number of cores utilized
    • Multi-job processing on grid
    • Other grid worker options
    • Testing a Grid Preset
    • Client-side: starting CLC jobs on the grid
    • Grid Integration Tips
    • Understanding memory settings
  • Model III: Single Server setup
  • Cloud settings
  • Configuring cloud presets
  • Workflow queuing options
    • Choosing a workflow queuing option
  • Job running options
    • Multi-job processing
    • Fairness factor
    • Concurrent jobs per node
    • Intermediate workflow result handling
• Status and management
  • User statistics
  • System statistics
  • Server maintenance
• Queue
• Audit log
• Server plugins
• BLAST
  • Adding directories for BLAST databases on the Server
  • Adding and removing BLAST databases
• 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
    • 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: MAFFT (containerized external application)
    • Create the Docker image
    • Test the Docker image locally
    • Upload the Docker image to a repository
    • Configure a containerized MAFFT 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
• Workflows
  • Installing and configuring workflows
  • Executing workflows
  • Updating workflows
• Genomics Analysis Portal
• Troubleshooting
  • Check setup
  • Bug reporting
• Command line tools
• Appendix
  • Use of multi-core computers
  • Database configurations
    • Installing JDBC drivers
    • Configuring MySQL
  • SSL and encryption
    • Enabling SSL on the server
    • Logging in using SSL from the Workbench
    • Logging in using SSL from the CLC Server Command Line Tools
  • Non-exclusive Algorithms
  • DRMAA libraries
    • DRMAA for SLURM
    • DRMAA for LSF
    • DRMAA for PBS Pro
    • DRMAA for OGE or SGE
  • Consumable Resources
  • Third party libraries
  • External network connections
    • Proxy settings
  • Read Mapper Reference Caching
  • Monitoring
    • Setting up JMX monitoring
    • Completed process metrics
    • Process execution metrics
    • Job node metrics
• Bibliography

Cloud settings

Cloud presets are configured in the Cloud settings area. Each cloud preset includes a job priority and information about how results should be handled. A tag can also be specified, which is then be added to all jobs submitted using that cloud preset. Users specify the cloud preset to use when submitting jobs to CLC Genomics Cloud Engine via their CLC Workbench or CLC Server Command Line Tools.

Before setting up cloud presets, please ensure the Cloud Server Plugin has been installed, and its plugin settings, which contain details of the cloud connection, have been configured.

The Cloud Server Plugin can be downloaded from https://digitalinsights.qiagen.com/plugins/cloud-plugin/.

Information about the Cloud Server Plugin settings is provided in the Cloud Plugin manual at: https://resources.qiagenbioinformatics.com/manuals/cloudplugin/current/index.php?manual=Configuring_AWS_CLC_Genomics_Cloud_Engine_settings.html.

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