• Manuals

Browse the manual

• Introduction
  • System requirements
  • Licensing
  • CLC Genomics Server
  • CLC Cancer Research Server solution
  • CLC Drug Discovery Server
• Installation
  • Quick installation guide
  • Installing and running the Server
    • Installing the Server software
  • Silent installation
  • CLC Cancer Research Server solution - installation notes
    • On the server: Create reference data directory
    • Using the CLC Genomics Server web interface: Add reference data location
    • Using the CLC Cancer Research Workbench: Set up connection between CLC Cancer Research Workbench and your CLC Genomics Server
  • CLC Drug Discovery Server - installation notes
  • 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
• Configuring and administering the server
  • 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
  • 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
  • Audit log
  • Deployment of server information to CLC Workbenches
  • Server plugins
  • Queue
  • Job queuing options
    • Multi-job processing
    • Fairness factor
    • Concurrent jobs per node
• Managing users and groups
  • Logging in the first time and changing the root password
  • User authentication using the web interface
    • 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
  • User statistics
• 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
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
  • Filling in values
    • What happens when a clc object is copied to another data location?
    • Searching
• Job Distribution
  • Model I: Master server with dedicated job nodes
    • Overview
    • User credentials on a master-job node setup
    • Configuring your setup
    • Installing Server plugins
    • Distributed task execution
  • Model II: Master server submitting to grid nodes
    • Overview
    • 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
    • Distributed task execution 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
• BLAST
  • Adding directories for BLAST databases on the Server
  • Adding and removing BLAST databases
• External applications
  • Basic configuration
  • Post-processing
    • Configuring the selected post processing tool
  • Stream handling
  • Environment
    • Environmental Variables
    • Working directory
    • Execute as master process
  • Parameter flow
  • Running External Applications
    • Running from a CLC Workbench
    • Running from CLC Server Command Line Tools
  • Velvet Integration
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • Bowtie Integration
    • Installing Bowtie
    • Understanding the Bowtie configuration
    • Parameter overview
    • Setting path for temporary data
    • Tools for building index files
  • Troubleshooting
    • Checking the configuration
    • Check your third party application
    • Is your Import/Export directory configured?
    • Check your naming
• Workflows
  • Installing and configuring workflows
  • Executing workflows
  • Automatic update of workflow elements
• Command line tools
• Appendix
  • Use of multi-core computers
  • Troubleshooting
    • Check set-up
    • 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
  • Parallel Algorithms
  • Third party libraries
• Bibliography

On the server: Create reference data directory

• You must create a directory on the server hard drive. This directory is where the CLC Cancer Research Workbench reference data will be stored. Please note that the name of the directory must be "CLC_References".

---