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
Bibliography
Zerbino and Birney, 2008
Zerbino, D. R. and Birney, E. (2008).
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Res
, 18(5):821-829.
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