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• Introduction
• Installation
• Basic usage
• Handling passwords
• Managing SSL certificates
• Specifying locations of inputs, outputs and exports
  • Getting the ID form of a CLC URL
• Result files and connecting analyses in pipelines
• Launching workflows
  • General workflow launching information
  • Providing input data for analyses on a CLC Server
  • Saving workflow outputs and exporting results
  • Launching workflows with Iterate elements
• Emptying the recycling bin for a CLC Server File Location

Introduction

Welcome to the user manual of CLC Server Command Line Tools 24.0.2. The latest version of this user manual can be found in pdf and html formats at https://digitalinsights.qiagen.com/technical-support/manuals/

The CLC Server Command Line Tools provide a command line client for CLC Server solutions^1.1. Using this client, tasks can be started on CLC Servers, including bioinformatics analyses, data import and export, and utility data operations such as moving, renaming, and deleting data. Some data and maintenance related tasks can only be carried out by users in the admin group, such as emptying all users' recycling bins or installing plugins.

The CLC Server Command Line Tools is particularly well suited for work on production environments. Automation and consistency are well supported through inclusion of CLC Server Command Line Tools commands in scripts and the use of standard system tools for scheduling tasks.

CLC Server Command Line Tools commands are non-interactive: all data and parameter settings required are specified up front in the command, making it very quick to launch complex jobs once the desired settings have been determined.

Choosing a CLC Server client

We provide two types of clients for the CLC Server, the CLC Server Command Line Tools and the graphical CLC Workbenches. Here we outline some considerations that may be useful when considering which client type 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 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.
• For analysis consistency and running analyses in a hands off manner, either client can be used. With the CLC Server Command Line Tools, pipelines of tasks to be run on the CLC Server can be scripted. Using a CLC Workbench, pipelines of tasks can be specified in a workflow, which can then be run directly on the CLC Server or on the CLC Workbench itself. Workflows can also be installed on a CLC Server, and such workflows can be launched using either client type.
• Automation is supported by the CLC Server Command Line Tools, where standard scheduling tools can be used to schedule the launching of commands or scripts.

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Footnotes

... solutions^1.1

Like other client software, the CLC Server Command Line Tools would commonly be installed and used on systems other than the one that the CLC Server software is installed on, although there is no restriction requiring this.

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