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• Introduction
  • System requirements
  • Licensing
• Installation
  • Quick installation guide
  • Installing the database
    • Download and install a Database Management System
    • Create a new database and user/role
    • Initialize the database
  • Installing and running the Server
    • Installing the Server software
  • Silent installation
  • 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
  • Starting and stopping the server
    • Microsoft Windows
    • Mac OS X
    • Linux
  • Installing relevant plug-ins in the Workbench
• Configuring and administering the server
  • Logging into the administrative interface
  • Adding locations for saving data
    • Adding a database location
    • Adding a file system location
    • Rebuilding the index
  • Changing the listening port
  • Changing the tmp directory
    • Job node setups
  • Setting the amount of memory available for the JVM
  • Limiting the number of cpus available for use
  • Other configurations
    • HTTP settings
    • Audit log settings
    • Deployment of server information to CLC Workbenches
  • Server plug-ins
  • Queue
• Managing users and groups
  • Logging in the first time - 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 data
    • Setting permissions on a folder
    • Technical notes about permissions and security
  • Global permissions
• Job Distribution
  • Model I: Master server with execution nodes
    • Master and job nodes explained
    • User credentials on a master-job node setup
    • Configuring your setup
    • Installing Server plug-ins
  • Model II: Master server submitting to grid nodes
    • 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
    • Other grid worker options
    • Testing a Grid Preset
    • Client-side: starting CLC jobs on the grid
    • Grid Integration Tips
    • Understanding memory settings
• BLAST
  • Adding directories for storing BLAST databases
  • Adding and removing BLAST databases
• External applications
  • External applications integration: Basic configuration
  • External applications integration: Post-processing
  • External applications integration: Stream handling
  • External applications integration: Environment
    • Environmental Variables
    • Working directory
    • Execute as master process
  • External applications integration: Parameter flow
  • External applications integration: Velvet
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • 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
• Appendix
  • Troubleshooting
    • Check set-up
    • Bug reporting
  • Database configurations
    • Configurations for MySQL
  • SSL and encryption
    • Enabling SSL on the server
    • Logging in using SSL from the Workbench
    • Enabling redirection from non-ssl port to ssl-enabled port
    • Logging in using SSL from the CLC Server Command Line Tools
• Bibliography

External applications integration: Post-processing

This section is still being written.

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