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CLC Server Command Line Tools

Command Line Tools for the CLC Server


With a toolbox of Command Line Tools for the server, the advanced user can incorporate server-access in scripts, integrations etc. Furthermore it is possible to inspect and invoke all services and upload/download any data in virtually any format.

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The CLC Server Command Line Tools is a command-line client for the CLC Server. It is able to start analyses on the server, import and export data, and perform various data operations such as moving, renaming and deleting data on the server.

A typical work flow using the CLC Server Command Line Tools would be first to import sequencing data, second to run various analyses like read mapping, SNP detection or RNA-Seq, and third optionally to export the results.

In order to guide you to the most effective use of the CLC Server, we provide a set of recommendations for when to use the CLC Server Command Line Tools and when to use the CLC Genomics Workbench (which is the other client for the server based on a graphical user interface):

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  • The command-line tool is ideal for scripting pipelines of data analyses. By encapsulating the instructions to the server in a script, you can run all your data sets through the exact same pipeline of analyses, making this a consistent and effective framework for production settings. For the initial pilot runs to find the right parameter settings and do quality control, we recommend using the Workbench. Once the right settings have been validated, they can be incorporated into a script using the command-line tool.
  • For visualization and interpretation of data we recommend using the CLC Genomics Workbench since the command-line tool does not have any viewing capabilities.
  • The only way to visualize and interpret data with the command-line tool is to export the results into other file formats and use other applications to work with the files.
  • For explorative work we recommend using the workbench. The great number of parameters are easier to interpret using the graphical user interface, and because selection and management of data can be quite tedious using the command-line tool. The graphical user interface has more constraints to guide correct choices of parameters and combination of parameters, and these constraints are not all there in the command-line tool. If you are familiar with stand-alone command-line applications, you will find the user experience of CLC Server Command Line Tools quite different and less efficient for exploratory work.