The CLC Server Command Line Tools is a command-line client for the CLC Genomics Server1.1. The CLC Server Command Line Tools, and in particular 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 data
- Run analyses such as read mapping, SNP detection or RNA-Seq
- (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:
- For visualization and interpretation of data we recommend the CLC Genomics Workbench. The only way to visualize and interpret data when you have worked using the CLC Server Command Line Tools is to export the results into file formats that can be imported into visualization tools.
- For explorative work we recommend using the CLC Genomics Workbench. The numerous parameters are easier to interpret using the graphical interface, and selection and management of data is more intuitive through this interface for most users. 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.
- For automation and consistency, of particular utility in production environments, the CLC Server Command Line Tools client is recommended. In particular, you can script pipelines of analyses on the CLC Genomics Server, and then use these scripts for processing many data sets in a consistent manner. For initial pilot runs, it is often helpful to use the exploratory features of the CLC Genomics Workbench to determine quality control and parameter settings, and then incorporate these settings into a script using the CLC Server Command Line Tools.
- ... Server1.1
- 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.