The CLC Server Command Line Tools is a command-line client for the CLC Server solutions1.1. The CLC Server Command Line Tools provide the tools to start analyses and other tasks on CLC Servers, including data import and export, and utility 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:
- Import your sequence or structure data
- Run analyses such as read mapping, SNP detection, RNA-Seq, or Docking Ligands
- (Optionally) export the results to your local disk
Other clients available to run tasks on the CLC Server are the graphical CLC Workbenches. Below are recommendations for choosing which of these two types clients, the graphical or the command line, to use for your work:
- For visualization and interpretation of data we recommend using a CLC Workbench. If results are generated using the CLC Server Command Line Tools, then these can be viewed using a CLC Workbench that is connected to the same CLC Server the analyses were carried out on. Alternatively, the data can be exported and shared.
- For explorative work we recommend using a CLC Workbench. The effects of parameter changes, for example, are easier to interpret using the graphical interface. For many users, selection and management of data is also more intuitive through a graphical interface. In addition, the graphical user interface has more constraints to help guide reasonable choices of parameters and combination of parameters; these constraints are not all present in the CLC Server Command Line Tools.
- Automation and consistency in production environments can be supported by using the CLC Server Command Line Tools. In particular, you can script pipelines of analyses on the CLC Server, and then use these scripts for processing many data sets in a consistent manner. Consistency is also supported in the CLC Workbenches by executing Workflow analyses in batch runs, but automation is still best supported through use of the CLC Server Command Line Tools.
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- Like any other client software, the CLC Server Command Line Tools would most commonly be installed and used on systems other than the one that the CLC Server software is installed on, although there is no restriction meaning that this must be the case.