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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
    • Windows license download
    • macOS license download
    • Linux license download
    • Download a static license on a non-networked machine
  • Starting and stopping the server
    • Microsoft Windows
    • macOS
    • Linux
  • Installing the database
    • Download and install a Database Management System
    • Create a new database and user/role
    • Initialize the database
• 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
    • Database locations
    • Rebuilding the index
  • Accessing files on, and writing to, areas of the server filesystem
  • Direct data transfer from client systems
  • Direct data transfer from client systems
  • 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 using the Workbench
    • Managing users through the Workbench
    • Managing groups through the Workbench
• Access privileges and permissions
  • Controlling access to CLC Server data
    • Setting permissions on a folder
    • Recycle bin
    • 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
• 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
  • Job queuing options
    • Choosing between Classic and Single entity options
  • Job running options
    • Multi-job processing
    • Fairness factor
    • Concurrent jobs per node
• Status and management
  • User statistics
  • System statistics
  • Server maintenance
• Queue
• Audit log
• Server plugins
• BLAST
  • Adding directories for BLAST databases on the Server
  • Adding and removing BLAST databases
• External applications
  • General configuration of external applications
    • Parameter value configuration
    • Configuring export from the CLC Server for an external application
    • Handling the output of an external tool
    • High throughput sequencing importers and post processing tools
  • Stream handling
  • Environment
    • Environmental variables
    • Working directory
    • Execute as master process
  • End user interface
  • Using consistent reference data in external applications
  • Velvet integration
    • Installing Velvet
    • Running Velvet from the Workbench
    • Understanding the Velvet configuration
  • Bowtie integration
    • Installing Bowtie
    • Understanding the Bowtie configuration
    • Setting the path for temporary data
    • Tools for building index files
  • Import and export of external application configurations
  • 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
    • Checking the configuration
    • Check your third party application
    • Is your Import/Export directory configured?
    • Check for conflicts in the naming of the external application
• Workflows
  • Installing and configuring workflows
  • Executing workflows
  • Updating workflows
• Command line tools
• Appendix
  • Use of multi-core computers
  • Troubleshooting
    • Check setup
    • Bug reporting
  • Database configurations
    • Installing JDBC drivers
    • Configuring 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
  • 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
  • Monitoring
    • Setting up JMX monitoring
    • Completed process metrics
    • Process execution metrics
    • Job node metrics
• Bibliography

Troubleshooting external applications

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Subsections

• Checking the configuration
• Check your third party application
• Is your Import/Export directory configured?
• Check for conflicts in the naming of the external application

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