Manuals
Browse the manual
Introduction
System requirements
Licensing
CLC Genomics Server
Installation
Quick installation guide
Installing and running the Server
Installing the Server software
Installation modes - console and silent
Upgrading an existing installation
Upgrading between major versions
Allowing access through your firewall
Downloading a license
Download a static license on a non-networked machine
Starting and stopping the server
Microsoft Windows
macOS
Linux
Basic configuration
Logging into the administrative interface
Adding locations for saving data
File system locations
Reference data management
Enabling and disabling internal compression of CLC data
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 and groups using built-in authentication
User authentication via the Workbench for built-in authentication
Access privileges and permissions
Controlling group access to CLC Server data
Setting permissions on folders
Technical notes about permissions and security
Controlling access to the server, server 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 custom attributes
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
Workflow queuing options
Choosing a workflow queuing option
Job running options
Multi-job processing
Fairness factor
Concurrent jobs per node
Intermediate workflow result handling
Access to files outside CLC Server Locations
Import/export directories
Direct data transfer from client systems
AWS Connections in the CLC Server
Illumina BaseSpace
Workflows
Installing and configuring workflows
Executing workflows
Updating workflows
BLAST databases
Adding directories for BLAST databases on the Server
Adding and removing BLAST databases
Status and management
Downloading a license via the web interface
Download a static license on a non-networked machine
Server maintenance
User statistics
System statistics
Queue
Audit log
Server plugins
External applications
External application configurations
Configuring the containerized execution environment
Configuring external applications
Editing external applications
External command
High-throughput sequencing import / Post-processing
Stream handling
Failure strategy
Environment
End user interface
Management
Using consistent reference data in external applications
Import and export of external application configurations
Updating external application configurations
Example: Velvet (standard external application)
Installing Velvet
Running Velvet from the Workbench
Understanding the Velvet configuration
Example: Bowtie (standard external application)
Installing Bowtie
Understanding the Bowtie Map configuration
Setting the path for temporary data
Tools for building index files
Example: Kraken2 (containerized external application)
Extending the Kraken2 external application for paired data
Example: MAFFT (containerized external application)
External applications in workflows
Running external applications
Using a CLC Workbench to launch external applications
Using CLC Server Command Line Tools to launch external applications
Troubleshooting external applications
CLC Genomics Cloud Access
Browsing and searching for data
Browsing CLC Server data locations
Searching CLC Server data locations
Rebuilding the index
Browse a CLC Server import/export directory
Browse AWS S3 locations
Recycle bins
Troubleshooting
Check setup
Bug reporting
Command line tools
Appendix
Use of multi-core computers
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 SLURM
DRMAA for LSF
DRMAA for PBS Pro
DRMAA for OGE or SGE
Consumable Resources
Third party libraries
External network connections
Proxy settings
Read Mapper Reference Caching
Monitoring
Setting up JMX monitoring
Completed process metrics
Process execution metrics
Job node metrics
Bibliography
Model I: Master server with dedicated job nodes
Subsections
Overview: Model I
User credentials on a master-job node setup
Configuring your setup
Installing Server plugins on job nodes