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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
    • Client-server encrypted communication
    • Logging in using SSL from a CLC Workbench
    • Logging in using SSL from the CLC Server Command Line Tools
    • Master-job node encrypted communication
    • Master-grid node encrypted communication
  • 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
    • 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 a job node 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
    • 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
• Analysis automation
• 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

Model I: Master server with dedicated job nodes

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Subsections

• Overview: Model I
• User credentials on a master-job node setup
• Configuring a job node setup
• Installing Server plugins on job nodes

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