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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
Basic configuration
- Logging into the administrative interface
- Adding locations for saving 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
Job distribution
- Introduction to servers setups
- Model I: Master server with dedicated job nodes
- Model II: Master server submitting to grid nodes
- Model III: Single Server setup
- Workflow queuing options
  - Choosing a workflow queuing option
- Job running options
Access to files outside CLC Server Locations
- Import/export directories
- Direct data transfer from client systems
- AWS Connections
- 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
- Using consistent reference data in external applications
- Import and export of external application configurations
- Updating external application configurations
- Example: Velvet (standard external application)
- Example: Bowtie (standard external application)
- 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
- Non-exclusive Algorithms
- DRMAA libraries
- Consumable Resources
- Third party libraries
- External network connections
  - Proxy settings
- Read Mapper Reference Caching
- Monitoring
Bibliography

Browse a CLC Server import/export directory

Under the Browse server import/export directories, you can browse the data held in areas configured as import/export directories in the External data area, under the Configuration tab (figure 16.5).

If folder or file is selected, information about it is displayed below the file browser.

Image browse-importexport-via-server
Figure 16.5: Browse CLC server import/export directories via the web interface.