HomeCLC FAQ - CLC Genomics Server and Command Line ToolsCLC Command Line ToolsAre there any general tips about composing a command using the CLT?

5.2. Are there any general tips about composing a command using the CLT?

Information about how to compose and run CLC Command Line Tools (CLT) commands is covered in the manual, which you can find in HTML or PDF format:

PDF: http://www.clcbio.com/files/usermanuals/CLC_Server_Command_Line_Tools_User_Manual.pdf

HTML: http://www.clcsupport.com/clcservercommandlinetools/current/

In terms of building up your own commands when starting out, one approach would be to

  • refer to the Genomics Workbench manual for the particular analysis you plan to run - as the information there, and reference to the wizard (job setup) interface there can provide a good idea of what the options presented via the Command Line Tools mean, and then,

  • look at the usage information that is generated with a basic clcserver command.


How to access the usage information for the Command Line Tools is covered in the manual starting here:



In brief, if you submit a command of the following form:

clcserver -U <username> -W <password or passcode> -S <serverhost>

and your credentials were fine, the top level commands that can be run on your CLC Server should be printed to screen. That is, the commands options that could be provided as arguments to the  -A option, as well other major options (-C, -D, -G and so on).


As an example, say you were interested in running a de novo assembly.  The information returned above would let you know that the relevant option to use after the -A flag would be denovo_assembly

At that point, the command to find out more about how to set up the details of the de novo assembly could be determined by running a command of this form:

clcserver -U <username> -W <password or passcode> -S <serverhost> -A denovo_assembly

This would return the command line options relevant to de novo assembly.


The location of your input files on your Genomics Server, and the location you wish to write data to can be specified in a number of ways, and for the most part rely on clc urls.  This is described in the manual here:


In terms of data input for tools like de novo assembly, where you may have multiple input data objects containing sequence reads, you would enter your each sequence list (sets of reads) after its own -i flag.


The above is just a short summary of tips for getting started. We highly recommend referring to the manual if you plan to use the Command Line Tools for your own analyses.

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