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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
- Server display name
- Adding locations for saving data
- Changing the listening port
- SSL and encryption
  - Logging in using SSL from a CLC Workbench
  - Logging in using SSL from the CLC Server Command Line Tools
- 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
- External network connections
- Proxy settings
Managing users and groups
- Changing the root password
- User authentication for the CLC Server
- 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 processing
- 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 settings
Working with external data locations
- Import/export directories
- Direct data transfer from client systems
- AWS Connections in the CLC Server
- AWS S3 public buckets
- Browse AWS S3 locations
- Illumina BaseSpace
Working with CLC Server File System Locations
- Browsing CLC Server File System Locations
- Searching CLC Server File System Locations
  - Rebuilding the index
Workflows
- Installing and configuring workflows
- Executing workflows
- Updating workflows
BLAST databases
Status and management
- Downloading a license via the web interface
- 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: 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
Recycle bins
- Automatic cleanup of recycle bins
- Emptying recycle bins
- Recycle bin restrictions
Configuring CLC Workbench connections
Troubleshooting
- Check setup
- Bug reporting
Command line tools
Appendix
- Use of multi-core computers
- Non-exclusive Algorithms
- DRMAA libraries
- Consumable Resources
- Server system communication diagrams
- Third party libraries
- Read Mapper Reference Caching
- Monitoring
Bibliography

Tools for building index files

We have also included scripts and configurations for building index files using the external applications on CLC Server. This also includes the possibility of listing the index files available. To get these to work, please make sure the path to the Bowtie installation directory is correct.

The Bowtie distribution itself also includes scripts to download index files of various organisms.