Manuals
Browse the manual
Introduction
System requirements
Licensing
Latest improvements
Installation
Quick installation guide
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 plugins in the Workbench
Configuring and administering the server
Logging into the administrative interface
Adding locations for saving data
Adding a file system 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 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 plugins
Queue
Managing users and groups
Logging in the first time and 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 data
Setting permissions on a folder
Recycle bin
Technical notes about permissions and security
Global permissions
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 the sequence is copied to another data location?
Searching
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
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
External applications integration: Bowtie
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
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
DRMAA libraries
DRMAA for LSF
DRMAA for PBS Pro
DRMAA for OGE or SGE
Consumable Resources
Third party libraries
Bibliography
Adding locations for saving data
Before you can use the server for doing analyses you will need to add one or more locations for storing your data.
Subsections
Adding a file system location
Rebuilding the index
