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Browse the manual

• 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

Audit log settings

The audit log records all the actions performed in the web interface and through the Workbenches. Note that data management operations (copying, deleting and adding files) done through the Workbench are not recorded.

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