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• Introduction
  • System requirements
  • Licensing
  • CLC Genomics Server
  • Biomedical Genomics Server Extension
• Installation
  • Quick installation guide
  • Installing and running the Server
    • Installing the Server software
  • Installation modes - console and silent
  • Biomedical Genomics Server Extension - installation notes
    • On the server: Create reference data directory
    • Using the CLC Genomics Server web interface: Add reference data location
  • Upgrading an existing installation
    • Upgrading major versions
  • Allowing access through your firewall
  • Downloading a license
    • Windows license download
    • Mac OS license download
    • Linux license download
    • Download a static license on a non-networked machine
  • Starting and stopping the server
    • Microsoft Windows
    • Mac OS X
    • Linux
  • Installing relevant plugins in the Workbench
  • 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
    • Adding a file system location
    • Adding a database location
    • 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 using the web interface
    • Managing groups using the web interface
  • User authentication using the Workbench
    • Managing users through the Workbench
    • Managing groups through the Workbench
    • Adding users to a group
• 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 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 on single servers or job nodes
    • 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
  • Running External Applications
    • Running from a CLC Workbench
    • Running from CLC Server Command Line Tools
  • Import and export
    • Export
    • Import
  • Use of reference data in external applications
    • How to make use of reference data in external applications
    • Deletion of exported reference data
  • Velvet Integration
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • Bowtie Integration
    • Installing Bowtie
    • Understanding the Bowtie configuration
    • Setting path for temporary data
    • Tools for building index files
  • External Applications in Workflows
  • 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
  • Automatic update of workflow elements
• Command line tools
• Appendix
  • Use of multi-core computers
  • Troubleshooting
    • Check setup
    • Bug reporting
  • Database configurations
    • Getting and installing JDBC drivers
    • Configurations for 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 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

Installing the database

For CLC Server solutions where the license includes the add-on CLC Bioinformatics Database, support for data management in an SQL-type database is available. This section describes how to install and setup CLC Bioinformatics Database for the CLC Server.

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Subsections

• Download and install a Database Management System
• Create a new database and user/role
• Initialize the database

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