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• Introduction
  • System requirements
  • Licensing
  • Latest improvements
• Installation
  • Quick installation guide
  • Installing the database
    • Download and install a Database Management System
    • Create a new database and user/role
    • Initialize the database
  • 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
    • Download a static license on a non-networked machine
  • 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 database location
    • Adding a file system location
    • Rebuilding the index
  • Accessing files on, and writing to, areas of the server filesystem
  • Setting up BLAST databases for CLC Science Server
  • 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
  • Audit log
  • Deployment of server information to CLC Workbenches
  • Server plugins
  • Queue
  • Multi-job Processing
• Managing users and groups
  • Logging in the first time and changing 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 a clc object 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 plugins
  • 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
    • 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
• BLAST
  • Adding directories for BLAST databases on the Server
  • Adding and removing BLAST databases
• External applications
  • External applications integration: Basic configuration
  • External applications integration: Post-processing
    • Configuring the selected post processing tool
  • 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
  • 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
• Command line tools
• Command line tools
  • Algorithms
    • add_att_b_sites
    • assemble_sanger_sequences
    • boxplot
    • bp_reaction
    • convert_to_dna
    • convert_to_rna
    • create_histogram
    • create_sequence_statistics
    • empirical_analysis_dge
    • extract_annotations
    • find_open_reading_frames
    • find_primer_binding_sites
    • gaussian_statistical_analysis
    • kmer_tree_construction
    • lr_reaction
    • ml_phylogeny
    • model_testing
    • principal_components
    • proportion_statistical_analysis
    • reference_assemble_sanger_sequences
    • reverse_complement_sequence
    • reverse_sequence
    • secondary_peak_calling
    • translate_to_protein
  • Core tasks
  • Dataoperations
    • chmod
    • cp
    • empty_recycle_bin
    • history
    • list_data_locations
    • list_import_locations
    • ls
    • mkdir
    • move
    • mv
    • rename
    • rm
    • search
  • Importers
    • ace
    • automaticimport
    • blast_db
    • bsml
    • chp
    • clc
    • clustalw
    • cm5
    • embl
    • excel
    • expression_annotation
    • expression_data_table
    • expressionarray
    • externalfile
    • fasta
    • fasta_alignment
    • gcg
    • gck
    • genbank
    • gene_ontology
    • illumina_annotation
    • illumina_expression
    • lasergene
    • msf
    • netaffx
    • newick
    • nexus
    • pdb_import
    • phylib
    • pir
    • raw_sequence
    • rna_structure
    • sequence_csv
    • soft_geo_sample
    • soft_geo_series
    • staden
    • strider
    • swissprot
    • table_csv
    • text
    • trace
    • zip
  • Exporters
• Appendix
  • 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
  • Third party libraries
• Bibliography

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