Introduction

The CLC Server Command Line Tools is a command-line client for the CLC Genomics 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 might be:

  1. Import your sequence data
  2. Run analyses such as read mapping, SNP detection or RNA-Seq
  3. (Optionally) export the results to your local disk

Another client available to run tasks on the CLC Genomics Server is the graphical CLC Genomics Workbench. Below are recommendations for choosing which of these two clients, the graphical or the command line, to use for your work:

This user manual begins with installation instructions followed by an explanation of the basics of operating the CLC Server Command Line Tools. Then, we provide an example script, which illustrates various aspects of how to use the analysis tools available on the server.



Subsections