• Manuals

Browse the manual

• 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

Command line tools

CLC Server Command Line Tools is a command-line client for the CLC Science Server that is described in detail in the CLC Server Command Line Tools manual found here (html version): http://www.clcsupport.com/clcservercommandlinetools/current/index.php?manual=Introduction.html or here (pdf version): http://www.clcbio.com/files/usermanuals/CLC_Server_Command_Line_Tools_User_Manual.pdf.

In the CLC Server Command Line Tools manual you can find information about how to download and install CLC Server Command Line Tools, the basic usage of the command line tools, and you can also find an example script that can be modified by the user.

/home/smikkelsen/workspaceTrunk/CommandLineTools/clcserver -S localhost -P 7777 -U root -W default -C 5000

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