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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
    • Windows license download
    • macOS license download
    • Linux license download
    • 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
  • 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
  • Job queuing options
    • Choosing between Classic and Single entity options
  • Job running options
    • Multi-job processing
    • Fairness factor
    • Concurrent jobs per node
• 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
  • General configuration of external applications
    • Parameter value configuration
    • Configuring export from the CLC Server for an external application
    • Handling the output of an external tool
    • High throughput sequencing importers and post processing tools
  • Stream handling
  • Environment
    • Environmental variables
    • Working directory
    • Execute as master process
  • End user interface
  • Using consistent reference data in external applications
  • Velvet integration
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • Bowtie integration
    • Installing Bowtie
    • Understanding the Bowtie configuration
    • Setting the path for temporary data
    • Tools for building index files
  • Import and export of external application configurations
  • 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
    • Checking the configuration
    • Check your third party application
    • Is your Import/Export directory configured?
    • Check for conflicts in the naming of the external application
• Workflows
  • Installing and configuring workflows
  • Executing workflows
  • Updating workflows
• Command line tools
• Appendix
  • Use of multi-core computers
  • Troubleshooting
    • Check setup
    • Bug reporting
  • 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
  • Monitoring
    • Setting up JMX monitoring
    • Completed process metrics
    • Process execution metrics
    • Job node metrics
• Bibliography

System requirements

The system requirements of CLC Server are:

Server system

• Windows 7, Windows 8, Windows 10, Windows Server 2012, and Windows Server 2016
• OS X 10.10, 10.11 and macOS 10.12, 10.13, 10.14
• Linux: RHEL 6.7 and later, SUSE Linux Enterprise Server 11 and later. The software is expected to run without problem on other recent Linux systems, but we do not guarantee this.
• 64 bit
• For CLC Server setups that include job nodes and grid nodes, those nodes must run the same type of operating system as the master CLC Server.
• File system that supports file locking. Due to a bug in Java 10, CLC Genomics Server software in the 11.x release line should not be installed on a GPFS file system.

Server hardware requirements

• Intel or AMD CPU required
• Computer power: 2 cores required. 8 cores recommended.
• Memory: CLC Genomics Server: 4 GB RAM required, 16 GB RAM recommended.
• Disk space: 500 GB required. More needed if large amounts of data are analyzed.

Special memory requirements for working with genomes

The numbers below give minimum and recommended amounts for systems running mapping and analysis tasks. The requirements suggested are based on the genome size.

• E. coli K12 (4.6 megabases)
  • Minimum: 2 GB RAM
  • Recommended: 4 GB RAM
• C. elegans (100 megabases) and Arabidopsis thaliana (120 megabases)
  • Minimum: 2 GB RAM
  • Recommended: 4 GB RAM
• Zebrafish (1.5 gigabases)
  • Minimum: 2 GB RAM
  • Recommended: 4 GB RAM
• Human (3.2 gigabases) and Mouse (2.7 gigabases)
  • Minimum: 6 GB RAM
  • Recommended: 8 GB RAM

Special requirements for de novo assembly

De novo assembly may need more memory than stated above - this depends both on the number of reads and the complexity and size of the genome. See http://resources.qiagenbioinformatics.com/white-papers/White_paper_on_de_novo_assembly_4.pdf for examples of the memory usage of various data sets.

Special requirement for the shared filesystem used by the job node setup or grid integration

The file locking mechanism is required to ensure that all nodes see the latest version of the data stored on the shared filesystem.

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